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Structure of PDB 4kxn Chain A Binding Site BS02

Receptor Information
>4kxn Chain A (length=131) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADAGGDQFIHEQN
LNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAM
IRGAADGSRFQVWDYAEGEVETMLDRYFEAY
Ligand information
Ligand ID6K6
InChIInChI=1S/C15H18N5O8P/c21-11-9(5-27-29(23,24)25)28-15(12(11)22)20-7-19-10-13(17-6-18-14(10)20)16-4-8-2-1-3-26-8/h1-3,6-7,9,11-12,15,21-22H,4-5H2,(H,16,17,18)(H2,23,24,25)/t9-,11-,12-,15-/m1/s1
InChIKeyWDFCXEWULSQTFC-SDBHATRESA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(NCc4occc4)ncnc23
OpenEye OEToolkits 1.7.6c1cc(oc1)CNc2c3c(ncn2)n(cn3)C4C(C(C(O4)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.7.6c1cc(oc1)CNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OCC4OC(n2cnc1c(ncnc12)NCc3occc3)C(O)C4O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(NCc4occc4)ncnc23
FormulaC15 H18 N5 O8 P
NameN-(furan-2-ylmethyl)adenosine 5'-(dihydrogen phosphate)
ChEMBL
DrugBank
ZINC
PDB chain4kxn Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4kxn N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		S117 M119
Binding residue
(residue number reindexed from 1)		S98 M100
Annotation score1
Binding affinityMOAD: Kd=0.8uM
PDBbind-CN: -logKd/Ki=6.10,Kd=0.8uM
Enzymatic activity
Enzyme Commision number 3.2.2.-
Gene Ontology
Molecular Function
GO:0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity
Biological Process
GO:0009159 deoxyribonucleoside monophosphate catabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:4kxn, PDBe:4kxn, PDBj:4kxn
PDBsum4kxn
PubMed24260472
UniProtO35820|DNPH1_RAT 5-hydroxymethyl-dUMP N-hydrolase (Gene Name=Dnph1)

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