Structure of PDB 4yih Chain B Binding Site BS02

Receptor Information
>4yih Chain B (length=187) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRAL
RPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLL
KYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQE
ETPSWEHILFTCCHNRHLRRRLLSWSDNWREILDSKR
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 chain4yih Chain B Residue 203 [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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PDB4yih Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor
Resolution1.82 Å
Binding residue
(original residue number in PDB)		D12 F18 F44 L45 A46 R47 Y65 L102 L103 R132
Binding residue
(residue number reindexed from 1)		D9 F15 F41 L42 A43 R44 Y62 L99 L100 R129
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.66,Ki=21.7uM
Enzymatic activity
Catalytic site (original residue number in PDB) D10 D12 D145
Catalytic site (residue number reindexed from 1) D7 D9 D142
Enzyme Commision number 3.1.3.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008252 nucleotidase activity
GO:0008253 5'-nucleotidase activity
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0019103 pyrimidine nucleotide binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0050483 IMP 5'-nucleotidase activity
Biological Process
GO:0000255 allantoin metabolic process
GO:0006204 IMP catabolic process
GO:0006249 dCMP catabolic process
GO:0009117 nucleotide metabolic process
GO:0009223 pyrimidine deoxyribonucleotide catabolic process
GO:0009264 deoxyribonucleotide catabolic process
GO:0016311 dephosphorylation
GO:0043605 amide catabolic process
GO:0046050 UMP catabolic process
GO:0046055 dGMP catabolic process
GO:0046074 dTMP catabolic process
GO:0046079 dUMP catabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4yih, PDBe:4yih, PDBj:4yih
PDBsum4yih
PubMed
UniProtQ8TCD5|NT5C_HUMAN 5'(3')-deoxyribonucleotidase, cytosolic type (Gene Name=NT5C)

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