Chemical Components in the PDB

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VPM : Summary

Code

VPM

One-letter code

X

Molecule name

(2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid
OpenEye OEToolkits 1.7.6 (2S)-2-oxidanyl-2-propan-2-yl-butanedioic acid

Formula

C7 H12 O5

Formal charge

0

Molecular weight

176.167 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(O)(CC(=O)O)C(C)C
SMILES CACTVS 3.385 CC(C)[C](O)(CC(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC(C)C(CC(=O)O)(C(=O)O)O
Canonical SMILES CACTVS 3.385 CC(C)[C@@](O)(CC(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)[C@@](CC(=O)O)(C(=O)O)O

IUPAC InChI

InChI=1S/C7H12O5/c1-4(2)7(12,6(10)11)3-5(8)9/h4,12H,3H2,1-2H3,(H,8,9)(H,10,11)/t7-/m0/s1

IUPAC InChI key

BITYXLXUCSKTJS-ZETCQYMHSA-N
VPM

wwPDB Information

Atom count

24 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-03-04

Last modified at

2014-08-15

Status

Released

Obsoleted

Not Assigned



VPM : Atoms of Molecule

Total Number of Atoms: 24
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAA C CAA N N N 0 2.85 -0.068 -0.743
2 CAK C CAK N N N 0 1.685 -0.997 -0.394
3 CAB C CAB N N N 0 1.891 -1.567 1.011
4 CAL C CAL S N N 0 0.374 -0.211 -0.438
5 CAJ C CAJ N N N 0 0.477 0.989 0.467
6 OAF O OAF N N N 0 0.711 0.823 1.778
7 OAD O OAD N N N 0 0.349 2.102 0.013
8 OAG O OAG N N N 0 0.124 0.223 -1.777
9 CAH C CAH N N N 0 -0.774 -1.107 0.031
10 CAI C CAI N N N 0 -2.066 -0.332 -0.013
11 OAE O OAE N N N 0 -2.068 0.819 -0.382
12 OAC O OAC N N N 0 -3.214 -0.92 0.357
13 H1 H H1 N N N 0 2.891 0.749 -0.022
14 H2 H H2 N N N 0 3.784 -0.628 -0.711
15 H3 H H3 N N N 0 2.703 0.338 -1.744
16 H4 H H4 N N N 0 1.644 -1.814 -1.115
17 H5 H H5 N N N 0 1.933 -0.75 1.732
18 H6 H H6 N N N 0 1.062 -2.229 1.26
19 H7 H H7 N N N 0 2.825 -2.127 1.043
20 H8 H H8 N N N 0 0.769 1.622 2.319
21 H9 H H9 N N N 0 0.045 -0.499 -2.416
22 H10 H H10 N N N 0 -0.849 -1.974 -0.624
23 H11 H H11 N N N 0 -0.583 -1.437 1.052
24 H12 H H12 N N N 0 -4.017 -0.383 0.312



VPM : Chemical Bonds

Total Number of Bonds: 23
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAB CAK C C sing 1.53 N N
2 CAA CAK C C sing 1.53 N N
3 OAG CAL O C sing 1.43 N N
4 CAK CAL C C sing 1.53 N N
5 CAL CAJ C C sing 1.51 N N
6 CAL CAH C C sing 1.53 N N
7 OAD CAJ O C doub 1.21 N N
8 CAJ OAF C O sing 1.34 N N
9 OAE CAI O C doub 1.21 N N
10 OAC CAI O C sing 1.34 N N
11 CAI CAH C C sing 1.51 N N
12 CAA H1 C H sing 1.09 N N
13 CAA H2 C H sing 1.09 N N
14 CAA H3 C H sing 1.09 N N
15 CAK H4 C H sing 1.09 N N
16 CAB H5 C H sing 1.09 N N
17 CAB H6 C H sing 1.09 N N
18 CAB H7 C H sing 1.09 N N
19 OAF H8 O H sing 0.97 N N
20 OAG H9 O H sing 0.97 N N
21 CAH H10 C H sing 1.09 N N
22 CAH H11 C H sing 1.09 N N
23 OAC H12 O H sing 0.97 N N



VPM : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VPM 4ov9 Open in New Window Bound ligand 1 1