Chemical Components in the PDB

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IGP : Summary

Code

IGP

One-letter code

X

Molecule name

INDOLE-3-GLYCEROL PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,3S)-2,3-dihydroxy-3-(1H-indol-3-yl)propyl dihydrogen phosphate
OpenEye OEToolkits 1.5.0 [(2R,3S)-2,3-dihydroxy-3-(1H-indol-3-yl)propyl] dihydrogen phosphate

Formula

C11 H14 N O6 P

Formal charge

0

Molecular weight

287.206 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)C(O)c2c1ccccc1nc2
SMILES CACTVS 3.341 O[CH](CO[P](O)(O)=O)[CH](O)c1c[nH]c2ccccc12
SMILES OpenEye OEToolkits 1.5.0 c1ccc2c(c1)c(c[nH]2)C(C(COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@H](CO[P](O)(O)=O)[C@@H](O)c1c[nH]c2ccccc12
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc2c(c1)c(c[nH]2)[C@@H]([C@@H](COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C11H14NO6P/c13-10(6-18-19(15,16)17)11(14)8-5-12-9-4-2-1-3-7(8)9/h1-5,10-14H,6H2,(H2,15,16,17)/t10-,11+/m1/s1

IUPAC InChI key

NQEQTYPJSIEPHW-MNOVXSKESA-N
IGP

wwPDB Information

Atom count

33 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



IGP : Atoms of Molecule

Total Number of Atoms: 33
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -0.229 -0.254 1.815
2 C2 C C2 R N N 0 -0.309 0.315 0.397
3 C3 C C3 S N N 0 -0.84 -0.758 -0.554
4 CD1 C CD1 N Y N 0 -1.969 0.431 -2.5
5 CD2 C CD2 N Y N 0 0.139 -0.228 -2.963
6 CE2 C CE2 N Y N 0 -0.391 0.408 -4.099
7 CE3 C CE3 N Y N 0 1.437 -0.741 -2.994
8 CG C CG N Y N 0 -0.918 -0.197 -1.95
9 CH2 C CH2 N Y N 0 1.673 0.021 -5.249
10 CZ2 C CZ2 N Y N 0 0.393 0.529 -5.241
11 CZ3 C CZ3 N Y N 0 2.19 -0.611 -4.127
12 H11 H 1H1 N N N 0 -1.222 -0.567 2.138
13 H12 H 2H1 N N N 0 0.442 -1.113 1.824
14 H2 H H2 N N N 0 -0.981 1.173 0.388
15 H3 H H3 N N N 0 -0.168 -1.616 -0.544
16 HD1 H HD1 N N N 0 -2.91 0.618 -2.003
17 HE3 H HE3 N N N 0 1.845 -1.235 -2.125
18 HH2 H HH2 N N N 0 2.281 0.115 -6.137
19 HN1 H HN1 N N N 0 -2.275 1.268 -4.382
20 HO2 H HO2 N N N 0 1.554 -0.062 -0.0020
21 HO3 H HO3 N N N 0 -2.704 -0.381 -0.154
22 HOP1 H 1HOP N N N 0 0.895 0.726 6.09
23 HOP2 H 2HOP N N N 0 -1.708 0.406 4.608
24 HZ2 H HZ2 N N N 0 0.0 1.019 -6.12
25 HZ3 H HZ3 N N N 0 3.196 -1.004 -4.149
26 NE1 N NE1 N Y N 0 -1.673 0.8 -3.784
27 O2 O O2 N N N 0 0.992 0.724 -0.024
28 O3 O O3 N N N 0 -2.142 -1.168 -0.131
29 OP1 O OP1 N N N 0 0.877 1.163 5.227
30 OP2 O OP2 N N N 0 -1.153 -0.385 4.604
31 OP3 O OP3 N N N 0 1.226 -1.089 4.144
32 OP4 O OP4 N N N 0 0.266 0.748 2.704
33 P P P N N N 0 0.324 0.083 4.17



IGP : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 OP4 C O sing 1.43 N N
2 C1 C2 C C sing 1.53 N N
3 C1 H11 C H sing 1.09 N N
4 C1 H12 C H sing 1.09 N N
5 P OP1 P O sing 1.61 N N
6 P OP2 P O sing 1.61 N N
7 P OP3 P O doub 1.48 N N
8 P OP4 P O sing 1.61 N N
9 OP1 HOP1 O H sing 0.97 N N
10 OP2 HOP2 O H sing 0.97 N N
11 C2 O2 C O sing 1.43 N N
12 C2 C3 C C sing 1.53 N N
13 C2 H2 C H sing 1.09 N N
14 O2 HO2 O H sing 0.97 N N
15 C3 O3 C O sing 1.43 N N
16 C3 CG C C sing 1.51 N N
17 C3 H3 C H sing 1.09 N N
18 O3 HO3 O H sing 0.97 N N
19 CG CD2 C C sing 1.46 N Y
20 CG CD1 C C doub 1.34 N Y
21 CD2 CE2 C C doub 1.41 N Y
22 CD2 CE3 C C sing 1.4 N Y
23 CE2 NE1 C N sing 1.38 N Y
24 CE2 CZ2 C C sing 1.39 N Y
25 CE3 CZ3 C C doub 1.37 N Y
26 CE3 HE3 C H sing 1.08 N N
27 CD1 NE1 C N sing 1.37 N Y
28 CD1 HD1 C H sing 1.08 N N
29 NE1 HN1 N H sing 0.97 N N
30 CZ2 CH2 C C doub 1.38 N Y
31 CZ2 HZ2 C H sing 1.08 N N
32 CZ3 CH2 C C sing 1.39 N Y
33 CZ3 HZ3 C H sing 1.08 N N
34 CH2 HH2 C H sing 1.08 N N



IGP : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
IGP 1a53 Open in New Window Bound ligand 1 1
IGP 1a5b Open in New Window Bound ligand 1 1
IGP 1kfb Open in New Window Bound ligand 1 1
IGP 1qoq Open in New Window Bound ligand 1 1
IGP 2rh9 Open in New Window Bound ligand 1 1
IGP 2rhg Open in New Window Bound ligand 1 1
IGP 3t44 Open in New Window Bound ligand 1 1