BioLiP

Receptor Information

>1khz Chain B (length=202) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERG
HAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVED
VARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIH
GLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNE
WA

Ligand ID

ADV

InChI

InChI=1S/C16H25N5O13P2/c17-13-8-14(19-3-18-13)21(4-20-8)15-11(24)9(22)6(33-15)1-31-35(27,28)5-36(29,30)32-2-7-10(23)12(25)16(26)34-7/h3-4,6-7,9-12,15-16,22-26H,1-2,5H2,(H,27,28)(H,29,30)(H2,17,18,19)/t6-,7-,9-,10-,11-,12-,15-,16+/m1/s1

InChIKey

ZPZRETFSCSWNDT-DBXCYWGHSA-N

SMILES

Software	SMILES
CACTVS 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)O)N
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
ACDLabs 10.04	O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)CP(=O)(O)OCC4OC(O)C(O)C4O

Formula

C16 H25 N5 O13 P2

Name

ALPHA-BETA METHYLENE ADP-RIBOSE;
AMPCPR;
{[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-(3,4,5-TRIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL) ESTER

PDB chain

1khz Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	1khz Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.
Resolution	2.04 Å
Binding residue (original residue number in PDB)	F28 F29 R56 R79 A96 G97 E112 E139 E162 E164
Binding residue (residue number reindexed from 1)	F21 F22 R49 R72 A89 G90 E105 E132 E155 E157
Annotation score	3

Enzyme Commision number

3.6.1.13: ADP-ribose diphosphatase.

	Molecular Function
GO:0000287	magnesium ion binding
GO:0005515	protein binding
GO:0016462	pyrophosphatase activity
GO:0016787	hydrolase activity
GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0019144	ADP-sugar diphosphatase activity
GO:0042803	protein homodimerization activity
GO:0046872	metal ion binding
GO:0047631	ADP-ribose diphosphatase activity

	Biological Process
GO:0006753	nucleoside phosphate metabolic process
GO:0009408	response to heat
GO:0019693	ribose phosphate metabolic process

	Cellular Component
GO:0005829	cytosol

PDB	RCSB:1khz, PDBe:1khz, PDBj:1khz
PDBsum	1khz
PubMed	12135348
UniProt	Q93K97\|ADPP_ECOLI ADP-ribose pyrophosphatase (Gene Name=nudF)

[Back to BioLiP]

Structure of PDB 1khz Chain B Binding Site BS03