Chemical Components in the PDB

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VH0 : Summary

Code

VH0

One-letter code

P

Molecule name

(2S,4S)-4-[4-(aminomethyl)-1,2,3-triazol-1-yl]pyrrolidine-2-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (4S)-4-[4-(aminomethyl)-1H-1,2,3-triazol-1-yl]-L-proline
OpenEye OEToolkits 1.9.2 (2S,4S)-4-[4-(aminomethyl)-1,2,3-triazol-1-yl]pyrrolidine-2-carboxylic acid

Formula

C8 H13 N5 O2

Formal charge

0

Molecular weight

211.221 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C2NCC(n1nnc(c1)CN)C2
SMILES CACTVS 3.385 NCc1cn(nn1)[CH]2CN[CH](C2)C(O)=O
SMILES OpenEye OEToolkits 1.9.2 c1c(nnn1C2CC(NC2)C(=O)O)CN
Canonical SMILES CACTVS 3.385 NCc1cn(nn1)[C@@H]2CN[C@@H](C2)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.9.2 c1c(nnn1[C@H]2C[C@H](NC2)C(=O)O)CN

IUPAC InChI

InChI=1S/C8H13N5O2/c9-2-5-4-13(12-11-5)6-1-7(8(14)15)10-3-6/h4,6-7,10H,1-3,9H2,(H,14,15)/t6-,7-/m0/s1

IUPAC InChI key

JFEVBUPMGGCXQM-BQBZGAKWSA-N

Is part of

JKT
VH0

wwPDB Information

Atom count

28 (15 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

PRO

Defined at

2013-04-23

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



VH0 : Atoms of Molecule

Total Number of Atoms: 28
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N11 N N11 N N N 0 1.942 0.434 -1.437
2 C23 C C23 N N N 0 0.805 1.378 -1.408
3 C10 C C10 S N N 0 2.536 0.473 -0.076
4 C8 C C8 N N N 0 3.318 -0.786 0.2
5 O9 O O9 N N N 0 3.127 -1.774 -0.47
6 C25 C C25 N N N 0 1.296 0.56 0.849
7 C24 C C24 S N N 0 0.337 1.477 0.056
8 N26 N N26 N Y N 0 -1.042 1.001 0.183
9 N27 N N27 N Y N 0 -1.924 1.454 1.003
10 N28 N N28 N Y N 0 -3.033 0.819 0.858
11 C30 C C30 N Y N 0 -1.61 0.013 -0.547
12 C29 C C29 N Y N 0 -2.884 -0.099 -0.103
13 C31 C C31 N N N 0 -3.929 -1.066 -0.598
14 N32 N N32 N N N 0 -3.943 -2.255 0.264
15 H231 H H231 N N N 0 1.126 2.358 -1.762
16 H232 H H232 N N N 0 -0.0060 1.003 -2.032
17 H10 H H10 N N N 0 3.17 1.352 0.042
18 H24 H H24 N N N 0 0.417 2.505 0.41
19 H251 H H251 N N N 0 0.854 -0.425 0.996
20 H252 H H252 N N N 0 1.56 1.013 1.805
21 H30 H H30 N N N 0 -1.14 -0.571 -1.325
22 H311 H H311 N N N 0 -4.908 -0.587 -0.572
23 H312 H H312 N N N 0 -3.696 -1.361 -1.62
24 H32 H H32 N N N 0 -4.637 -2.919 -0.047
25 H2 H H2 N N Y 0 1.633 -0.498 -1.67
26 H3 H H3 N N Y 0 -3.03 -2.681 0.309
27 OXT O OXT N N Y 0 4.225 -0.809 1.188
28 HXT H HXT N N Y 0 4.702 -1.639 1.327



VH0 : Chemical Bonds

Total Number of Bonds: 29
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N11 C23 N C sing 1.48 N N
2 N11 C10 N C sing 1.49 N N
3 C23 C24 C C sing 1.54 N N
4 C10 C8 C C sing 1.51 N N
5 C10 C25 C C sing 1.55 N N
6 C8 O9 C O doub 1.21 N N
7 C25 C24 C C sing 1.55 N N
8 C24 N26 C N sing 1.46 N N
9 N26 N27 N N sing 1.29 N Y
10 N26 C30 N C sing 1.35 N Y
11 N27 N28 N N doub 1.29 N Y
12 N28 C29 N C sing 1.34 N Y
13 C30 C29 C C doub 1.35 N Y
14 C29 C31 C C sing 1.51 N N
15 C31 N32 C N sing 1.47 N N
16 C23 H231 C H sing 1.09 N N
17 C23 H232 C H sing 1.09 N N
18 C10 H10 C H sing 1.09 N N
19 C24 H24 C H sing 1.09 N N
20 C25 H251 C H sing 1.09 N N
21 C25 H252 C H sing 1.09 N N
22 C30 H30 C H sing 1.08 N N
23 C31 H311 C H sing 1.09 N N
24 C31 H312 C H sing 1.09 N N
25 N32 H32 N H sing 1.01 N N
26 N11 H2 N H sing 1.01 N N
27 N32 H3 N H sing 1.01 N N
28 C8 OXT C O sing 1.34 N N
29 OXT HXT O H sing 0.97 N N



VH0 : Used in PDB Entries

Total Number of PDB Entries: 0
Ligand Code PDB Entry ID Type Total Distinct
VH0 4bcc Open in New Window Sub-component 1 1