Chemical Components in the PDB

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M3L : Summary

Code

M3L

One-letter code

K

Molecule name

N-TRIMETHYLLYSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[(5S)-5-amino-5-carboxypentyl]-N,N-dimethylmethanaminium
OpenEye OEToolkits 1.5.0 [(5S)-5-amino-6-hydroxy-6-oxo-hexyl]-trimethyl-azanium

Formula

C9 H21 N2 O2

Formal charge

1

Molecular weight

189.275 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(N)CCCC[N+](C)(C)C
SMILES CACTVS 3.341 C[N+](C)(C)CCCC[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 C[N+](C)(C)CCCCC(C(=O)O)N
Canonical SMILES CACTVS 3.341 C[N+](C)(C)CCCC[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[N+](C)(C)CCCC[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C9H20N2O2/c1-11(2,3)7-5-4-6-8(10)9(12)13/h8H,4-7,10H2,1-3H3/p+1/t8-/m0/s1

IUPAC InChI key

MXNRLFUSFKVQSK-QMMMGPOBSA-O
M3L

wwPDB Information

Atom count

34 (13 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

LYS

Defined at

1999-07-08

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



M3L : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N N N N 0 2.673 -1.806 -0.237
2 CA C CA S N N 0 2.588 -0.365 -0.509
3 CB C CB N N N 0 1.322 0.202 0.136
4 CG C CG N N N 0 0.09 -0.41 -0.535
5 CD C CD N N N 0 -1.176 0.157 0.11
6 CE C CE N N N 0 -2.408 -0.455 -0.56
7 NZ N NZ N N N 1 -3.623 0.09 0.059
8 C C C N N N 0 3.798 0.327 0.065
9 O O O N N N 0 4.447 -0.211 0.93
10 OXT O OXT N N Y 0 4.153 1.541 -0.384
11 CM1 C CM1 N N N 0 -3.648 1.549 -0.111
12 CM2 C CM2 N N N 0 -3.632 -0.237 1.491
13 CM3 C CM3 N N N 0 -4.806 -0.498 -0.585
14 H H 1HN N N N 0 2.704 -1.91 0.766
15 H2 H 2HN N N Y 0 1.802 -2.211 -0.544
16 HA H HA N N N 0 2.553 -0.2 -1.586
17 HB2 H 1HB N N N 0 1.304 1.285 0.01
18 HB3 H 2HB N N N 0 1.315 -0.04 1.198
19 HG2 H 1HG N N N 0 0.109 -1.492 -0.409
20 HG3 H 2HG N N N 0 0.097 -0.167 -1.598
21 HD2 H 1HD N N N 0 -1.194 1.24 -0.016
22 HD3 H 2HD N N N 0 -1.182 -0.085 1.173
23 HE2 H 1HE N N N 0 -2.389 -1.537 -0.435
24 HE3 H 2HE N N N 0 -2.401 -0.212 -1.623
25 HXT H HXT N N Y 0 4.929 1.985 -0.016
26 HM11 H 1HM1 N N N 0 -2.771 1.985 0.367
27 HM12 H 2HM1 N N N 0 -3.641 1.791 -1.173
28 HM13 H 3HM1 N N N 0 -4.55 1.953 0.349
29 HM21 H 1HM2 N N N 0 -4.534 0.167 1.95
30 HM22 H 2HM2 N N N 0 -3.614 -1.32 1.616
31 HM23 H 3HM2 N N N 0 -2.755 0.199 1.968
32 HM31 H 1HM3 N N N 0 -4.799 -0.255 -1.648
33 HM32 H 2HM3 N N N 0 -4.788 -1.581 -0.459
34 HM33 H 3HM3 N N N 0 -5.708 -0.094 -0.126



M3L : Chemical Bonds

Total Number of Bonds: 33
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA N C sing 1.47 N N
2 N H N H sing 1.01 N N
3 N H2 N H sing 1.01 N N
4 CA CB C C sing 1.53 N N
5 CA C C C sing 1.51 N N
6 CA HA C H sing 1.09 N N
7 CB CG C C sing 1.53 N N
8 CB HB2 C H sing 1.09 N N
9 CB HB3 C H sing 1.09 N N
10 CG CD C C sing 1.53 N N
11 CG HG2 C H sing 1.09 N N
12 CG HG3 C H sing 1.09 N N
13 CD CE C C sing 1.53 N N
14 CD HD2 C H sing 1.09 N N
15 CD HD3 C H sing 1.09 N N
16 CE NZ C N sing 1.47 N N
17 CE HE2 C H sing 1.09 N N
18 CE HE3 C H sing 1.09 N N
19 NZ CM1 N C sing 1.47 N N
20 NZ CM2 N C sing 1.47 N N
21 NZ CM3 N C sing 1.47 N N
22 C O C O doub 1.21 N N
23 C OXT C O sing 1.34 N N
24 OXT HXT O H sing 0.97 N N
25 CM1 HM11 C H sing 1.09 N N
26 CM1 HM12 C H sing 1.09 N N
27 CM1 HM13 C H sing 1.09 N N
28 CM2 HM21 C H sing 1.09 N N
29 CM2 HM22 C H sing 1.09 N N
30 CM2 HM23 C H sing 1.09 N N
31 CM3 HM31 C H sing 1.09 N N
32 CM3 HM32 C H sing 1.09 N N
33 CM3 HM33 C H sing 1.09 N N



M3L : Used in PDB Entries

Total Number of PDB Entries: 311
Ligand Code PDB Entry ID Type Total Distinct
M3L 1ccr Open in New Window Polymer component 2 2
M3L 1chh Open in New Window Polymer component 1 1
M3L 1chi Open in New Window Polymer component 1 1
M3L 1chj Open in New Window Polymer component 1 1
M3L 1cie Open in New Window Polymer component 1 1
M3L 1cif Open in New Window Polymer component 1 1
M3L 1cig Open in New Window Polymer component 1 1
M3L 1cih Open in New Window Polymer component 1 1
M3L 1crg Open in New Window Polymer component 1 1
M3L 1crh Open in New Window Polymer component 1 1
M3L 1cri Open in New Window Polymer component 1 1
M3L 1crj Open in New Window Polymer component 1 1
M3L 1csu Open in New Window Polymer component 1 1
M3L 1csv Open in New Window Polymer component 1 1
M3L 1csw Open in New Window Polymer component 1 1
M3L 1csx Open in New Window Polymer component 1 1
M3L 1cty Open in New Window Polymer component 1 1
M3L 1ctz Open in New Window Polymer component 1 1
M3L 1fhb Open in New Window Polymer component 1 1
M3L 1irv Open in New Window Polymer component 1 1
M3L 1irw Open in New Window Polymer component 1 1
M3L 1kne Open in New Window Polymer component 1 1
M3L 1kyo Open in New Window Polymer component 1 1
M3L 1pdq Open in New Window Polymer component 1 1
M3L 1pfb Open in New Window Polymer component 1 1
M3L 1prw Open in New Window Polymer component 1 1
M3L 1rap Open in New Window Polymer component 1 1
M3L 1raq Open in New Window Polymer component 1 1
M3L 1up5 Open in New Window Polymer component 2 1
M3L 1ycc Open in New Window Polymer component 1 1
M3L 1yea Open in New Window Polymer component 1 1
M3L 1yeb Open in New Window Polymer component 1 1
M3L 1yfc Open in New Window Polymer component 1 1
M3L 1yic Open in New Window Polymer component 1 1
M3L 1ytc Open in New Window Polymer component 1 1
M3L 2b2t Open in New Window Polymer component 1 1
M3L 2b2u Open in New Window Polymer component 1 1
M3L 2b2w Open in New Window Polymer component 1 1
M3L 2f6j Open in New Window Polymer component 1 1
M3L 2fuu Open in New Window Polymer component 1 1
M3L 2g6q Open in New Window Polymer component 1 1
M3L 2gfa Open in New Window Polymer component 2 1
M3L 2h23 Open in New Window Bound ligand 3 1
M3L 2h6q Open in New Window Polymer component 2 1
M3L 2h9p Open in New Window Polymer component 1 1
M3L 2jmj Open in New Window Polymer component 1 1
M3L 2k17 Open in New Window Polymer component 1 1
M3L 2kgi Open in New Window Polymer component 1 1
M3L 2l11 Open in New Window Polymer component 1 1
M3L 2l12 Open in New Window Polymer component 1 1
M3L 2l1b Open in New Window Polymer component 1 1
M3L 2l3r Open in New Window Polymer component 1 1
M3L 2l75 Open in New Window Polymer component 1 1
M3L 2lbm Open in New Window Polymer component 1 1
M3L 2lgk Open in New Window Polymer component 1 1
M3L 2m0o Open in New Window Polymer component 1 1
M3L 2oq6 Open in New Window Polymer component 2 1
M3L 2os2 Open in New Window Polymer component 2 1
M3L 2p5b Open in New Window Polymer component 2 1
M3L 2pnx Open in New Window Polymer component 2 1
M3L 2q8c Open in New Window Polymer component 2 1
M3L 2q8e Open in New Window Polymer component 2 1
M3L 2qic Open in New Window Polymer component 1 1
M3L 2qqs Open in New Window Polymer component 2 1
M3L 2rr4 Open in New Window Polymer component 1 1
M3L 2rsn Open in New Window Polymer component 1 1
M3L 2rvn Open in New Window Polymer component 1 1
M3L 2v83 Open in New Window Polymer component 2 1
M3L 2v85 Open in New Window Polymer component 2 1
M3L 2v86 Open in New Window Polymer component 2 1
M3L 2v87 Open in New Window Polymer component 2 1
M3L 2v89 Open in New Window Polymer component 2 1
M3L 2vnf Open in New Window Polymer component 2 1
M3L 2x4w Open in New Window Polymer component 1 1
M3L 2x4x Open in New Window Polymer component 4 1
M3L 2x4y Open in New Window Polymer component 8 1
M3L 2ybp Open in New Window Polymer component 2 1
M3L 2ybs Open in New Window Polymer component 2 1
M3L 2ycc Open in New Window Polymer component 1 1
M3L 2yk3 Open in New Window Polymer component 3 1
M3L 2yyr Open in New Window Polymer component 1 1
M3L 3ask Open in New Window Polymer component 3 1
M3L 3avr Open in New Window Polymer component 1 1
M3L 3c6w Open in New Window Polymer component 2 1
M3L 3cx5 Open in New Window Polymer component 1 1
M3L 3cxh Open in New Window Polymer component 1 1
M3L 3db3 Open in New Window Polymer component 1 1
M3L 3dm1 Open in New Window Polymer component 4 1
M3L 3fdt Open in New Window Polymer component 1 1
M3L 3g7l Open in New Window Polymer component 1 1
M3L 3gl6 Open in New Window Polymer component 1 1
M3L 3gv6 Open in New Window Polymer component 1 1
M3L 3h91 Open in New Window Polymer component 2 1
M3L 3i90 Open in New Window Polymer component 2 1
M3L 3i91 Open in New Window Polymer component 1 1
M3L 3iiw Open in New Window Polymer component 1 1
M3L 3iiy Open in New Window Polymer component 1 1
M3L 3ij0 Open in New Window Polymer component 1 1
M3L 3ij1 Open in New Window Polymer component 1 1
M3L 3jpx Open in New Window Polymer component 1 1
M3L 3jzg Open in New Window Polymer component 1 1
M3L 3jzh Open in New Window Polymer component 1 1
M3L 3k26 Open in New Window Polymer component 1 1
M3L 3k27 Open in New Window Polymer component 1 1
M3L 3kqi Open in New Window Polymer component 1 1
M3L 3kv4 Open in New Window Polymer component 1 1
M3L 3lqj Open in New Window Polymer component 2 1
M3L 3m5a Open in New Window Polymer component 1 1
M3L 3me9 Open in New Window Polymer component 2 1
M3L 3mea Open in New Window Polymer component 1 1
M3L 3meu Open in New Window Polymer component 2 1
M3L 3mev Open in New Window Polymer component 2 1
M3L 3mo8 Open in New Window Polymer component 1 1
M3L 3mp1 Open in New Window Polymer component 1 1
M3L 3n9l Open in New Window Polymer component 1 1
M3L 3n9n Open in New Window Polymer component 2 1
M3L 3n9o Open in New Window Polymer component 1 1
M3L 3n9p Open in New Window Polymer component 2 1
M3L 3n9q Open in New Window Polymer component 1 1
M3L 3o7a Open in New Window Polymer component 1 1
M3L 3qby Open in New Window Polymer component 1 1
M3L 3qj6 Open in New Window Polymer component 1 1
M3L 3ql9 Open in New Window Polymer component 1 1
M3L 3qla Open in New Window Polymer component 2 1
M3L 3qo2 Open in New Window Polymer component 4 1
M3L 3r93 Open in New Window Polymer component 4 1
M3L 3sow Open in New Window Polymer component 2 1
M3L 3u4s Open in New Window Polymer component 2 1
M3L 3u5n Open in New Window Polymer component 2 1
M3L 3u5o Open in New Window Polymer component 8 1
M3L 3u5p Open in New Window Polymer component 8 1
M3L 3v0s Open in New Window Polymer component 2 2
M3L 4bd3 Open in New Window Polymer component 1 1
M3L 4dws Open in New Window Polymer component 13 13
M3L 4ezh Open in New Window Polymer component 2 1
M3L 4gng Open in New Window Polymer component 2 1
M3L 4gy5 Open in New Window Polymer component 2 1
M3L 4h75 Open in New Window Polymer component 1 1
M3L 4hcz Open in New Window Polymer component 2 1
M3L 4hon Open in New Window Polymer component 2 1
M3L 4igq Open in New Window Polymer component 1 1
M3L 4iur Open in New Window Polymer component 1 1
M3L 4l58 Open in New Window Polymer component 1 1
M3L 4l7x Open in New Window Polymer component 1 1
M3L 4lxl Open in New Window Polymer component 1 1
M3L 4mn3 Open in New Window Polymer component 1 1
M3L 4mzf Open in New Window Polymer component 1 1
M3L 4mzg Open in New Window Polymer component 2 1
M3L 4mzh Open in New Window Polymer component 1 1
M3L 4n4h Open in New Window Polymer component 1 1
M3L 4n4i Open in New Window Polymer component 1 1
M3L 4nw2 Open in New Window Polymer component 2 1
M3L 4o62 Open in New Window Polymer component 1 1
M3L 4pl6 Open in New Window Polymer component 2 1
M3L 4pli Open in New Window Polymer component 2 1
M3L 4pll Open in New Window Polymer component 2 1
M3L 4qq4 Open in New Window Polymer component 2 1
M3L 4quf Open in New Window Polymer component 6 1
M3L 4qx8 Open in New Window Polymer component 2 1
M3L 4qxb Open in New Window Polymer component 2 1
M3L 4u68 Open in New Window Polymer component 3 1
M3L 4uy4 Open in New Window Polymer component 2 1
M3L 4v2v Open in New Window Polymer component 2 1
M3L 4v2w Open in New Window Polymer component 1 1
M3L 4w5a Open in New Window Polymer component 3 1
M3L 4x3e Open in New Window Polymer component 1 1
M3L 4x3k Open in New Window Polymer component 2 1
M3L 4x3s Open in New Window Polymer component 2 1
M3L 4yhp Open in New Window Polymer component 2 1
M3L 4yhy Open in New Window Bound ligand 2 1
M3L 4yhz Open in New Window Polymer component 1 1
M3L 4z0r Open in New Window Polymer component 1 1
M3L 5ciu Open in New Window Polymer component 2 1
M3L 5d6y Open in New Window Polymer component 4 1
M3L 5hyn Open in New Window Polymer component 4 1
M3L 5ix1 Open in New Window Polymer component 2 1
M3L 5kjh Open in New Window Polymer component 1 1
M3L 5kkl Open in New Window Polymer component 1 1
M3L 5kpj Open in New Window Polymer component 2 2
M3L 5ls6 Open in New Window Polymer component 4 1
M3L 5lug Open in New Window Polymer component 4 1
M3L 5ly2 Open in New Window Polymer component 4 1
M3L 5m5g Open in New Window Polymer component 1 1
M3L 5mz2 Open in New Window Polymer component 8 1
M3L 5n69 Open in New Window Polymer component 2 1
M3L 5n9z Open in New Window Polymer component 8 1
M3L 5o8w Open in New Window Polymer component 1 1
M3L 5oya Open in New Window Polymer component 8 2
M3L 5svx Open in New Window Polymer component 1 1
M3L 5tdw Open in New Window Polymer component 1 1
M3L 5ttw Open in New Window Polymer component 2 1
M3L 5wfc Open in New Window Polymer component 1 1
M3L 5wle Open in New Window Polymer component 1 1
M3L 5wxh Open in New Window Polymer component 2 1
M3L 5xfq Open in New Window Polymer component 2 1
M3L 5xfr Open in New Window Polymer component 2 1
M3L 5xmy Open in New Window Polymer component 2 1
M3L 5y20 Open in New Window Polymer component 1 1
M3L 5y5w Open in New Window Polymer component 3 1
M3L 5yc4 Open in New Window Polymer component 1 1
M3L 5yko Open in New Window Polymer component 1 1
M3L 5yy9 Open in New Window Polymer component 2 1
M3L 5z8l Open in New Window Polymer component 1 1
M3L 5znp Open in New Window Polymer component 2 1
M3L 5znr Open in New Window Polymer component 2 1
M3L 6asz Open in New Window Polymer component 1 1
M3L 6at0 Open in New Window Polymer component 1 1
M3L 6bhe Open in New Window Polymer component 1 1
M3L 6bhi Open in New Window Polymer component 1 1
M3L 6c23 Open in New Window Polymer component 1 1
M3L 6c24 Open in New Window Polymer component 1 1
M3L 6c4w Open in New Window Polymer component 1 1
M3L 6d07 Open in New Window Polymer component 2 1
M3L 6ftl Open in New Window Polymer component 4 1
M3L 6h8p Open in New Window Polymer component 2 1
M3L 6iis Open in New Window Polymer component 2 1
M3L 6ip4 Open in New Window Polymer component 1 1
M3L 6j2p Open in New Window Polymer component 4 1
M3L 6ldv Open in New Window Polymer component 1 1
M3L 6ldw Open in New Window Polymer component 2 1
M3L 6ldx Open in New Window Polymer component 1 1
M3L 6ldy Open in New Window Polymer component 2 1
M3L 6lqe Open in New Window Polymer component 1 1
M3L 6lqf Open in New Window Polymer component 1 1
M3L 6mha Open in New Window Polymer component 1 1
M3L 6pzv Open in New Window Polymer component 2 1
M3L 6v2h Open in New Window Polymer component 6 1
M3L 6v3n Open in New Window Polymer component 2 1
M3L 6v3x Open in New Window Polymer component 1 1
M3L 6v3y Open in New Window Polymer component 1 1
M3L 6v41 Open in New Window Polymer component 1 1
M3L 6vil Open in New Window Polymer component 4 1
M3L 6wat Open in New Window Polymer component 30 1
M3L 6wau Open in New Window Polymer component 6 1
M3L 6wav Open in New Window Polymer component 4 1
M3L 6wkr Open in New Window Polymer component 2 1
M3L 6x5i Open in New Window Polymer component 70 1
M3L 6ysy Open in New Window Polymer component 1 1
M3L 6z1r Open in New Window Polymer component 8 1
M3L 6z1u Open in New Window Polymer component 8 1
M3L 6zbb Open in New Window Polymer component 8 1
M3L 6zg7 Open in New Window Polymer component 8 1
M3L 6zg8 Open in New Window Polymer component 8 1
M3L 6zik Open in New Window Polymer component 8 1
M3L 6ziq Open in New Window Polymer component 3 1
M3L 6zit Open in New Window Polymer component 3 1
M3L 6zmr Open in New Window Polymer component 8 1
M3L 6zna Open in New Window Polymer component 32 1
M3L 6zpo Open in New Window Polymer component 8 1
M3L 6zqm Open in New Window Polymer component 8 1
M3L 6zqn Open in New Window Polymer component 8 1
M3L 7ajb Open in New Window Polymer component 16 1
M3L 7ajc Open in New Window Polymer component 16 1
M3L 7ajd Open in New Window Polymer component 16 1
M3L 7aje Open in New Window Polymer component 16 1
M3L 7ajf Open in New Window Polymer component 16 1
M3L 7ajg Open in New Window Polymer component 16 1
M3L 7ajh Open in New Window Polymer component 16 1
M3L 7aji Open in New Window Polymer component 16 1
M3L 7ajj Open in New Window Polymer component 16 1
M3L 7bqz Open in New Window Polymer component 8 2
M3L 7bu9 Open in New Window Polymer component 4 1
M3L 7cce Open in New Window Polymer component 1 1
M3L 7cna Open in New Window Polymer component 4 4
M3L 7ebk Open in New Window Polymer component 1 1
M3L 7ef2 Open in New Window Polymer component 2 1
M3L 7lbk Open in New Window Polymer component 2 1
M3L 7lmk Open in New Window Polymer component 4 1
M3L 7m10 Open in New Window Polymer component 1 1
M3L 7o7y Open in New Window Polymer component 1 1
M3L 7o7z Open in New Window Polymer component 1 1
M3L 7o80 Open in New Window Polymer component 1 1
M3L 7o81 Open in New Window Polymer component 1 1
M3L 7oat Open in New Window Polymer component 1 1
M3L 7td5 Open in New Window Polymer component 2 1
M3L 7vrf Open in New Window Polymer component 2 1
M3L 7vyw Open in New Window Polymer component 1 1
M3L 7yi1 Open in New Window Polymer component 2 1
M3L 7yi4 Open in New Window Polymer component 2 1
M3L 7yi5 Open in New Window Polymer component 2 1
M3L 7yk5 Open in New Window Polymer component 8 1
M3L 7zez Open in New Window Polymer component 1 1
M3L 7zjw Open in New Window Polymer component 1 1
M3L 7zjx Open in New Window Polymer component 1 1
M3L 8act Open in New Window Polymer component 4 2
M3L 8btk Open in New Window Polymer component 1 1
M3L 8ds8 Open in New Window Polymer component 2 1
M3L 8f8y Open in New Window Polymer component 2 1
M3L 8f8z Open in New Window Polymer component 2 1
M3L 8g5y Open in New Window Polymer component 1 1
M3L 8g5z Open in New Window Polymer component 4 4
M3L 8g60 Open in New Window Polymer component 4 4
M3L 8g61 Open in New Window Polymer component 1 1
M3L 8g6j Open in New Window Polymer component 4 4
M3L 8glp Open in New Window Polymer component 1 1
M3L 8hl7 Open in New Window Polymer component 1 1
M3L 8kd3 Open in New Window Polymer component 2 1
M3L 8kd4 Open in New Window Polymer component 2 1
M3L 8kd5 Open in New Window Polymer component 2 1
M3L 8kd6 Open in New Window Polymer component 2 1
M3L 8kd7 Open in New Window Polymer component 2 1
M3L 8p2k Open in New Window Polymer component 1 1
M3L 8qyp Open in New Window Polymer component 2 2
M3L 8qyq Open in New Window Polymer component 4 2
M3L 8qyr Open in New Window Polymer component 2 2
M3L 8qyu Open in New Window Polymer component 4 2
M3L 9baq Open in New Window Polymer component 2 1
M3L 9c0o Open in New Window Polymer component 1 1
M3L 9f1b Open in New Window Polymer component 1 1
M3L 9f1c Open in New Window Polymer component 1 1
M3L 9f1d Open in New Window Polymer component 1 1