Structure of PDB 4yik Chain A Binding Site BS02

Receptor Information
>4yik Chain A (length=201) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNAASGGRALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFW
VSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDV
FICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDD
RPDITGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKR
P
Ligand information
Ligand ID2O2
InChIInChI=1S/C18H20N2O11P2/c21-16-11(6-7-32(23,24)25)9-20(17(22)19-16)15-8-13-14(30-15)10-29-18(31-13,33(26,27)28)12-4-2-1-3-5-12/h1-7,9,13-15H,8,10H2,(H,19,21,22)(H2,23,24,25)(H2,26,27,28)/b7-6+/t13-,14-,15-,18-/m1/s1
InChIKeyAYSYVLQGVXZPIY-OAIWFRFLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)[C@]2(OC[C@@H]3[C@H](O2)C[C@@H](O3)N4C=C(C(=O)NC4=O)/C=C/P(=O)(O)O)P(=O)(O)O
CACTVS 3.385O[P](O)(=O)/C=C/C1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
ACDLabs 12.01O=P(O)(O)/C=C/C1=CN(C(=O)NC1=O)C4OC2C(OC(OC2)(c3ccccc3)P(=O)(O)O)C4
OpenEye OEToolkits 1.7.6c1ccc(cc1)C2(OCC3C(O2)CC(O3)N4C=C(C(=O)NC4=O)C=CP(=O)(O)O)P(=O)(O)O
CACTVS 3.385O[P](O)(=O)C=CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
FormulaC18 H20 N2 O11 P2
Name1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINCZINC000263620255
PDB chain4yik Chain A Residue 306 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yik Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor
Resolution1.483 Å
Binding residue
(original residue number in PDB)		D41 D43 F49 F75 W76 V77 W96 S131 I133 K134 R163
Binding residue
(residue number reindexed from 1)		D15 D17 F23 F49 W50 V51 W70 S105 I107 K108 R137
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.89,Ki=0.128uM
Enzymatic activity
Catalytic site (original residue number in PDB) D41 D43 D176
Catalytic site (residue number reindexed from 1) D15 D17 D150
Enzyme Commision number 3.1.3.-
Gene Ontology
Molecular Function
GO:0008253 5'-nucleotidase activity
Biological Process
GO:0009264 deoxyribonucleotide catabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:4yik, PDBe:4yik, PDBj:4yik
PDBsum4yik
PubMed
UniProtQ9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)

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