Chemical Components in the PDB

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1GP : Summary

Code

1GP

One-letter code

X

Molecule name

SN-GLYCEROL-1-PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-2,3-dihydroxypropyl dihydrogen phosphate
OpenEye OEToolkits 1.5.0 [(2S)-2,3-dihydroxypropyl] dihydrogen phosphate

Formula

C3 H9 O6 P

Formal charge

0

Molecular weight

172.074 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)CO
SMILES CACTVS 3.341 OC[CH](O)CO[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 C(C(COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.341 OC[C@H](O)CO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@@H](COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)/t3-/m0/s1

IUPAC InChI key

AWUCVROLDVIAJX-VKHMYHEASA-N
1GP

wwPDB Information

Atom count

19 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-12-27

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



1GP : Atoms of Molecule

Total Number of Atoms: 19
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C3 C C3 N N N 0 2.998 0.727 -0.321
2 O3 O O3 N N N 0 2.157 -1.521 -0.034
3 C2 C C2 S N N 0 1.931 -0.157 0.327
4 O2 O O2 N N Y 0 4.28 0.4 0.221
5 C1 C C1 N N N 0 0.546 0.277 -0.159
6 O1P O O1P N N N 0 -0.457 -0.47 0.533
7 O2P O O2P N N N 0 -1.908 -0.1 -1.498
8 O3P O O3P N N N 0 -3.056 -0.858 0.619
9 O4P O O4P N N N 0 -2.098 1.579 0.378
10 P P P N N N 0 -1.88 0.035 -0.024
11 H31 H 1H3 N N N 0 2.775 1.774 -0.118
12 H32 H 2H3 N N N 0 3.005 0.558 -1.397
13 HO3 H HO3 N N N 0 2.102 -1.567 -0.999
14 H2 H H2 N N N 0 1.984 -0.055 1.411
15 HO2 H HO2 N N N 0 4.922 0.978 -0.213
16 H11 H 1H1 N N N 0 0.408 1.34 0.038
17 H12 H 2H1 N N N 0 0.463 0.091 -1.229
18 HO3P H HO3P N N N 0 -3.889 -0.523 0.259
19 HO4P H HO4P N N N 0 -2.072 1.622 1.343



1GP : Chemical Bonds

Total Number of Bonds: 18
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C3 C2 C C sing 1.53 N N
2 C3 O2 C O sing 1.43 N N
3 C3 H31 C H sing 1.09 N N
4 C3 H32 C H sing 1.09 N N
5 O3 C2 O C sing 1.43 N N
6 O3 HO3 O H sing 0.97 N N
7 C2 C1 C C sing 1.53 N N
8 C2 H2 C H sing 1.09 N N
9 O2 HO2 O H sing 0.97 N N
10 C1 O1P C O sing 1.43 N N
11 C1 H11 C H sing 1.09 N N
12 C1 H12 C H sing 1.09 N N
13 O1P P O P sing 1.61 N N
14 O2P P O P doub 1.48 N N
15 O3P P O P sing 1.61 N N
16 O3P HO3P O H sing 0.97 N N
17 O4P P O P sing 1.61 N N
18 O4P HO4P O H sing 0.97 N N



1GP : Used in PDB Entries

Total Number of PDB Entries: 21
Ligand Code PDB Entry ID Type Total Distinct
1GP 2f6x Open in New Window Bound ligand 2 1
1GP 2vyv Open in New Window Bound ligand 1 1
1GP 2y61 Open in New Window Bound ligand 1 1
1GP 2y62 Open in New Window Bound ligand 1 1
1GP 3ew5 Open in New Window Bound ligand 3 1
1GP 3k42 Open in New Window Bound ligand 2 1
1GP 3vzy Open in New Window Bound ligand 1 1
1GP 3w00 Open in New Window Bound ligand 1 1
1GP 4jej Open in New Window Bound ligand 1 1
1GP 4mm1 Open in New Window Bound ligand 6 1
1GP 4nae Open in New Window Bound ligand 2 1
1GP 4rgq Open in New Window Bound ligand 1 1
1GP 4xc3 Open in New Window Bound ligand 2 1
1GP 5wcx Open in New Window Bound ligand 2 1
1GP 6dgm Open in New Window Bound ligand 2 1
1GP 6jo3 Open in New Window Bound ligand 1 1
1GP 6xnc Open in New Window Bound ligand 1 1
1GP 6xoy Open in New Window Bound ligand 1 1
1GP 6xrh Open in New Window Bound ligand 1 1
1GP 6xt0 Open in New Window Bound ligand 1 1
1GP 8spf Open in New Window Bound ligand 1 1