Chemical Components in the PDB

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PLT : Summary

Code

PLT

One-letter code

X

Molecule name

[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-L-TRYPTOPHANE

Systematic names

ProgramVersionName
ACDLabs 10.04 (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-tryptophan
OpenEye OEToolkits 1.5.0 (2S)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-(1H-indol-3-yl)propanoic acid

Formula

C19 H20 N3 O7 P

Formal charge

0

Molecular weight

433.352 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCc1cnc(c(O)c1/C=N/C(C(=O)O)Cc3c2ccccc2nc3)C
SMILES CACTVS 3.341 Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](Cc2c[nH]c3ccccc23)C(O)=O)c1O
SMILES OpenEye OEToolkits 1.5.0 Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(Cc2c[nH]c3c2cccc3)C(=O)O)O
Canonical SMILES CACTVS 3.341 Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](Cc2c[nH]c3ccccc23)C(O)=O)c1O
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@@H](Cc2c[nH]c3c2cccc3)C(=O)O)O

IUPAC InChI

InChI=1S/C19H20N3O7P/c1-11-18(23)15(13(8-20-11)10-29-30(26,27)28)9-22-17(19(24)25)6-12-7-21-16-5-3-2-4-14(12)16/h2-5,7-9,17,21,23H,6,10H2,1H3,(H,24,25)(H2,26,27,28)/b22-9+/t17-/m0/s1

IUPAC InChI key

MFRRQHVPLFTBMS-NUYDQDRBSA-N
PLT

wwPDB Information

Atom count

50 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



PLT : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 2.921 1.631 2.832
2 C2 C C2 N Y N 0 3.498 1.55 1.651
3 C2A C C2A N N N 0 4.816 2.243 1.417
4 C3 C C3 N Y N 0 2.905 0.838 0.618
5 O3 O O3 N N N 0 3.503 0.758 -0.597
6 C4 C C4 N Y N 0 1.68 0.193 0.855
7 C4A C C4A N N N 0 1.011 -0.581 -0.207
8 C5 C C5 N Y N 0 1.11 0.311 2.128
9 C6 C C6 N Y N 0 1.769 1.045 3.093
10 C5A C C5A N N N 0 -0.205 -0.353 2.44
11 O4P O O4P N N N 0 -0.566 -0.081 3.796
12 P P P N N N 0 -1.974 -0.817 4.059
13 O1P O O1P N N N 0 -1.818 -2.273 3.838
14 O2P O O2P N N N 0 -2.443 -0.552 5.576
15 O3P O O3P N N N 0 -3.081 -0.236 3.045
16 N N N N N N 0 1.555 -0.677 -1.376
17 CA C CA S N N 0 0.891 -1.446 -2.432
18 C C C N N N 0 1.792 -2.569 -2.878
19 O O O N N N 0 1.315 -3.598 -3.293
20 OXT O OXT N N N 0 3.125 -2.425 -2.815
21 CB C CB N N N 0 0.592 -0.529 -3.619
22 CG C CG N Y N 0 -0.308 0.592 -3.173
23 CD1 C CD1 N Y N 0 0.078 1.785 -2.694
24 NE1 N NE1 N Y N 0 -1.017 2.546 -2.393
25 CE2 C CE2 N Y N 0 -2.167 1.844 -2.68
26 CZ2 C CZ2 N Y N 0 -3.522 2.138 -2.568
27 CH2 C CH2 N Y N 0 -4.459 1.202 -2.948
28 CZ3 C CZ3 N Y N 0 -4.065 -0.033 -3.442
29 CE3 C CE3 N Y N 0 -2.74 -0.343 -3.559
30 CD2 C CD2 N Y N 0 -1.773 0.592 -3.186
31 H2A1 H 1H2A N N N 0 5.632 1.564 1.662
32 H2A2 H 2H2A N N N 0 4.89 2.537 0.37
33 H2A3 H 3H2A N N N 0 4.878 3.129 2.048
34 HO3 H HO3 N N N 0 3.174 1.501 -1.12
35 H4A H H4A N N N 0 0.068 -1.067 -0.009
36 H6 H H6 N N N 0 1.335 1.14 4.077
37 H5A1 H 1H5A N N N 0 -0.976 0.035 1.774
38 H5A2 H 2H5A N N N 0 -0.111 -1.429 2.298
39 HOP2 H 2HOP N N N 0 -3.288 -1.009 5.691
40 HOP3 H 3HOP N N N 0 -3.152 0.711 3.222
41 HA H HA N N N 0 -0.041 -1.86 -2.048
42 HXT H HXT N N N 0 3.703 -3.145 -3.101
43 HB1 H 1HB N N N 0 1.525 -0.116 -4.003
44 HB2 H 2HB N N N 0 0.098 -1.101 -4.405
45 HD1 H HD1 N N N 0 1.104 2.097 -2.564
46 HNE H HNE N N N 0 -0.989 3.446 -2.033
47 HZ2 H HZ2 N N N 0 -3.838 3.097 -2.185
48 HH2 H HH2 N N N 0 -5.51 1.433 -2.86
49 HZ3 H HZ3 N N N 0 -4.813 -0.755 -3.735
50 HE3 H HE3 N N N 0 -2.441 -1.307 -3.944



PLT : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.32 N Y
2 N1 C6 N C sing 1.32 N Y
3 C2 C2A C C sing 1.51 N N
4 C2 C3 C C sing 1.39 N Y
5 C2A H2A1 C H sing 1.09 N N
6 C2A H2A2 C H sing 1.09 N N
7 C2A H2A3 C H sing 1.09 N N
8 C3 O3 C O sing 1.36 N N
9 C3 C4 C C doub 1.4 N Y
10 O3 HO3 O H sing 0.97 N N
11 C4 C4A C C sing 1.47 N N
12 C4 C5 C C sing 1.4 N Y
13 C4A N C N doub 1.29 E N
14 C4A H4A C H sing 1.08 N N
15 C5 C6 C C doub 1.38 N Y
16 C5 C5A C C sing 1.51 N N
17 C6 H6 C H sing 1.08 N N
18 C5A O4P C O sing 1.43 N N
19 C5A H5A1 C H sing 1.09 N N
20 C5A H5A2 C H sing 1.09 N N
21 O4P P O P sing 1.61 N N
22 P O1P P O doub 1.48 N N
23 P O2P P O sing 1.61 N N
24 P O3P P O sing 1.61 N N
25 O2P HOP2 O H sing 0.97 N N
26 O3P HOP3 O H sing 0.97 N N
27 N CA N C sing 1.47 N N
28 CA C C C sing 1.51 N N
29 CA CB C C sing 1.53 N N
30 CA HA C H sing 1.09 N N
31 C O C O doub 1.21 N N
32 C OXT C O sing 1.34 N N
33 OXT HXT O H sing 0.97 N N
34 CB CG C C sing 1.51 N N
35 CB HB1 C H sing 1.09 N N
36 CB HB2 C H sing 1.09 N N
37 CG CD1 C C doub 1.34 N Y
38 CG CD2 C C sing 1.47 N Y
39 CD1 NE1 C N sing 1.37 N Y
40 CD1 HD1 C H sing 1.08 N N
41 NE1 CE2 N C sing 1.38 N Y
42 NE1 HNE N H sing 0.97 N N
43 CE2 CZ2 C C doub 1.39 N Y
44 CE2 CD2 C C sing 1.41 N Y
45 CZ2 CH2 C C sing 1.38 N Y
46 CZ2 HZ2 C H sing 1.08 N N
47 CH2 CZ3 C C doub 1.39 N Y
48 CH2 HH2 C H sing 1.08 N N
49 CZ3 CE3 C C sing 1.37 N Y
50 CZ3 HZ3 C H sing 1.08 N N
51 CE3 CD2 C C doub 1.4 N Y
52 CE3 HE3 C H sing 1.08 N N



PLT : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
PLT 2tys Open in New Window Bound ligand 1 1
PLT 6am8 Open in New Window Bound ligand 2 1