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Receptor Information

>3bm4 Chain B (length=197) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GKQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGV
AVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRE
LEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKP
GDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHANA

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

3bm4 Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3bm4 Molecular Mechanism of ADP-Ribose Hydrolysis By Human NUDT5 From Structural and Kinetic Studies
Resolution	2.0 Å
Binding residue (original residue number in PDB)	W28 R51 R84 A96 G97 L98
Binding residue (residue number reindexed from 1)	W16 R39 R72 A84 G85 L86
Annotation score	3

Enzyme Commision number

2.7.7.96: ADP-D-ribose pyrophosphorylase.
3.6.1.13: ADP-ribose diphosphatase.
3.6.1.58: 8-oxo-dGDP phosphatase.

	Molecular Function
GO:0000287	magnesium ion binding
GO:0003723	RNA binding
GO:0005515	protein binding
GO:0016462	pyrophosphatase activity
GO:0016740	transferase activity
GO:0016779	nucleotidyltransferase activity
GO:0016787	hydrolase activity
GO:0017110	nucleoside diphosphate phosphatase activity
GO:0019144	ADP-sugar diphosphatase activity
GO:0030515	snoRNA binding
GO:0042802	identical protein binding
GO:0042803	protein homodimerization activity
GO:0044715	8-oxo-dGDP phosphatase activity
GO:0044716	8-oxo-GDP phosphatase activity
GO:0046872	metal ion binding
GO:0047631	ADP-ribose diphosphatase activity
GO:0140933	5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity

	Biological Process
GO:0006139	nucleobase-containing compound metabolic process
GO:0006338	chromatin remodeling
GO:0006753	nucleoside phosphate metabolic process
GO:0009117	nucleotide metabolic process
GO:0009191	ribonucleoside diphosphate catabolic process
GO:0019303	D-ribose catabolic process
GO:0019693	ribose phosphate metabolic process
GO:0055086	nucleobase-containing small molecule metabolic process
GO:1990966	ATP generation from poly-ADP-D-ribose

	Cellular Component
GO:0005634	nucleus
GO:0005829	cytosol
GO:0070062	extracellular exosome

PDB	RCSB:3bm4, PDBe:3bm4, PDBj:3bm4
PDBsum	3bm4
PubMed	18462755
UniProt	Q9UKK9\|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

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Structure of PDB 3bm4 Chain B Binding Site BS04