Chemical Components in the PDB

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WT2 : Summary

Code

WT2

One-letter code

X

Molecule name

(S)-2-AMINO-5-(2-OXOACETIMIDAMIDO)PENTANOIC ACID

Systematic names

ProgramVersionName
ACDLabs 12.01 N~5~-[(1Z)-2-oxoethanimidoyl]-L-ornithine
OpenEye OEToolkits 1.7.6 (2S)-2-azanyl-5-(2-oxidanylideneethanimidoylamino)pentanoic acid

Formula

C7 H13 N3 O3

Formal charge

0

Molecular weight

187.196 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)CCCNC(=[N@H])C=O
SMILES CACTVS 3.385 N[CH](CCCNC(=N)C=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 C(CC(C(=O)O)N)CNC(=N)C=O
Canonical SMILES CACTVS 3.385 N[C@@H](CCCNC(=N)C=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C(C[C@@H](C(=O)O)N)CNC(=N)C=O

IUPAC InChI

InChI=1S/C7H13N3O3/c8-5(7(12)13)2-1-3-10-6(9)4-11/h4-5H,1-3,8H2,(H2,9,10)(H,12,13)/t5-/m0/s1

IUPAC InChI key

JPSGSOHVMKIFBG-YFKPBYRVSA-N
WT2

wwPDB Information

Atom count

26 (13 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-02-02

Last modified at

2015-04-24

Status

Released

Obsoleted

Not Assigned



WT2 : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CH C CH N N N 0 -4.717 0.548 0.368
2 CZ C CZ N N N 0 -3.484 -0.156 -0.062
3 NH N NH N N N 0 -3.57 -1.255 -0.749
4 NE N NE N N N 0 -2.246 0.357 0.267
5 CD C CD N N N 0 -1.029 -0.338 -0.158
6 CG C CG N N N 0 0.197 0.434 0.334
7 CB C CB N N N 0 1.469 -0.292 -0.11
8 CA C CA S N N 0 2.695 0.48 0.381
9 C C C N N N 0 3.943 -0.297 0.052
10 OA2 O OA2 N N N 0 4.605 0.004 -0.913
11 OA1 O OA1 N N N 0 4.32 -1.324 0.83
12 HA H HA N N N 0 2.628 0.62 1.46
13 N N N N N N 0 2.745 1.791 -0.28
14 OH O OH N N N 0 -5.8 0.099 0.08
15 HA1 H HA1 N N N 0 5.128 -1.792 0.578
16 HN1 H HN1 N N N 0 3.509 2.346 0.075
17 HN2 H HN2 N N N 0 2.807 1.689 -1.281
18 HB1C H HB1C N N N 0 1.479 -1.297 0.312
19 HB2C H HB2C N N N 0 1.491 -0.354 -1.198
20 HG1C H HG1C N N N 0 0.187 1.439 -0.088
21 HG2C H HG2C N N N 0 0.175 0.496 1.422
22 HD1C H HD1C N N N 0 -1.018 -1.343 0.264
23 HD2C H HD2C N N N 0 -1.007 -0.401 -1.245
24 HH1N H HH1N N N N 0 -4.44 -1.615 -0.98
25 HH H HH N N N 0 -4.645 1.46 0.943
26 HNE H NEH N N N 0 -2.182 1.178 0.78



WT2 : Chemical Bonds

Total Number of Bonds: 25
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OA1 C O C sing 1.34 N N
2 C OA2 C O doub 1.21 N N
3 C CA C C sing 1.51 N N
4 CA N C N sing 1.47 N N
5 CA CB C C sing 1.53 N N
6 CB CG C C sing 1.53 N N
7 CG CD C C sing 1.53 N N
8 CD NE C N sing 1.46 N N
9 NE CZ N C sing 1.38 N N
10 CZ NH C N doub 1.3 N N
11 CZ CH C C sing 1.48 N N
12 CH OH C O doub 1.21 N N
13 OA1 HA1 O H sing 0.97 N N
14 CA HA C H sing 1.09 N N
15 N HN1 N H sing 1.01 N N
16 N HN2 N H sing 1.01 N N
17 CB HB1C C H sing 1.09 N N
18 CB HB2C C H sing 1.09 N N
19 CG HG1C C H sing 1.09 N N
20 CG HG2C C H sing 1.09 N N
21 CD HD1C C H sing 1.09 N N
22 CD HD2C C H sing 1.09 N N
23 NH HH1N N H sing 0.97 N N
24 CH HH C H sing 1.08 N N
25 NE HNE N H sing 0.97 N N



WT2 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
WT2 5agm Open in New Window Bound ligand 2 1