Chemical Components in the PDB

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9WV : Summary

Code

9WV

One-letter code

A

Molecule name

beta-alanyl-3-amino-L-alanine

Systematic names

ProgramVersionName
ACDLabs 12.01 beta-alanyl-3-amino-L-alanine
OpenEye OEToolkits 2.0.6 (2~{S})-3-azanyl-2-(3-azanylpropanoylamino)propanoic acid

Formula

C6 H13 N3 O3

Formal charge

0

Molecular weight

175.186 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 NCC(NC(=O)CCN)C(O)=O
SMILES CACTVS 3.385 NCCC(=O)N[CH](CN)C(O)=O
SMILES OpenEye OEToolkits 2.0.6 C(CN)C(=O)NC(CN)C(=O)O
Canonical SMILES CACTVS 3.385 NCCC(=O)N[C@@H](CN)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 C(CN)C(=O)N[C@@H](CN)C(=O)O

IUPAC InChI

InChI=1S/C6H13N3O3/c7-2-1-5(10)9-4(3-8)6(11)12/h4H,1-3,7-8H2,(H,9,10)(H,11,12)/t4-/m0/s1

IUPAC InChI key

GCVUIVWSQPUJMO-BYPYZUCNSA-N
9WV

wwPDB Information

Atom count

25 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

L-peptide linking

Type code

HETAIN

Is modified

Yes

Standard parent

ALA

Defined at

2017-06-20

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



9WV : Atoms of Molecule

Total Number of Atoms: 25
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N NDV N N N 0 -0.516 2.352 -0.505
2 CB C CB N N N 0 -1.692 1.472 -0.545
3 CA C CA S N N 0 -1.398 0.191 0.239
4 NDV N N N N N 0 -0.182 -0.435 -0.286
5 CEG C CEG N N N 0 1.027 -0.038 0.16
6 OEK O OEK N N N 0 1.108 0.837 0.995
7 CEH C CEH N N N 0 2.278 -0.682 -0.381
8 CEI C CEI N N N 0 3.503 -0.054 0.285
9 NEJ N NEJ N N N 0 4.723 -0.681 -0.241
10 C C C N N N 0 -2.556 -0.762 0.097
11 O O O N N N 0 -2.383 -1.853 -0.394
12 H H H1 N N N 0 -0.685 3.205 -1.017
13 H2 H H2 N N Y 0 -0.243 2.548 0.446
14 HB3 H HB1 N N N 0 -2.544 1.984 -0.098
15 HB2 H HB2 N N N 0 -1.921 1.219 -1.58
16 HA H HA N N N 0 -1.255 0.435 1.292
17 H1 H H N N N 0 -0.247 -1.135 -0.954
18 H8 H H8 N N N 0 2.257 -1.751 -0.169
19 H9 H H9 N N N 0 2.33 -0.526 -1.458
20 H10 H H10 N N N 0 3.524 1.015 0.073
21 H11 H H11 N N N 0 3.451 -0.209 1.363
22 H12 H H12 N N N 0 5.547 -0.283 0.184
23 H13 H H13 N N N 0 4.698 -1.682 -0.115
24 OXT O OXT N N Y 0 -3.779 -0.4 0.514
25 HXT H HXT N N Y 0 -4.49 -1.045 0.402



9WV : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CB N C sing 1.47 N N
2 CB CA C C sing 1.53 N N
3 CA NDV C N sing 1.46 N N
4 CA C C C sing 1.51 N N
5 O C O C doub 1.21 N N
6 NDV CEG N C sing 1.35 N N
7 CEH CEG C C sing 1.51 N N
8 CEH CEI C C sing 1.53 N N
9 CEG OEK C O doub 1.21 N N
10 NEJ CEI N C sing 1.47 N N
11 N H N H sing 1.01 N N
12 N H2 N H sing 1.01 N N
13 CB HB3 C H sing 1.09 N N
14 CB HB2 C H sing 1.09 N N
15 CA HA C H sing 1.09 N N
16 NDV H1 N H sing 0.97 N N
17 CEH H8 C H sing 1.09 N N
18 CEH H9 C H sing 1.09 N N
19 CEI H10 C H sing 1.09 N N
20 CEI H11 C H sing 1.09 N N
21 NEJ H12 N H sing 1.01 N N
22 NEJ H13 N H sing 1.01 N N
23 C OXT C O sing 1.34 N N
24 OXT HXT O H sing 0.97 N N



9WV : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
9WV 5w6r Open in New Window Polymer component 4 1
9WV 5w6t Open in New Window Polymer component 1 1