Structure of PDB 3bm4 Chain B Binding Site BS03

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 information
Ligand IDADV
InChIInChI=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
InChIKeyZPZRETFSCSWNDT-DBXCYWGHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(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 1.5.0c1nc(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 1.5.0c1nc(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 3.341Nc1ncnc2n(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 10.04O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)CP(=O)(O)OCC4OC(O)C(O)C4O
FormulaC16 H25 N5 O13 P2
NameALPHA-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
ChEMBL
DrugBankDB01975
ZINCZINC000015636817
PDB chain3bm4 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3bm4 Molecular Mechanism of ADP-Ribose Hydrolysis By Human NUDT5 From Structural and Kinetic Studies
Resolution2.0 Å
Binding residue
(original residue number in PDB)		W46 E47 D133 G135
Binding residue
(residue number reindexed from 1)		W34 E35 D121 G123
Annotation score3
Enzymatic activity
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.
Gene Ontology
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3bm4, PDBe:3bm4, PDBj:3bm4
PDBsum3bm4
PubMed18462755
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

[Back to BioLiP]