Structure of PDB 6g2n Chain B Binding Site BS02

Receptor Information
>6g2n Chain B (length=192) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRAL
RPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLL
KYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQE
ETPSWEHILFTCCHNRHLVLPPTRRRLLSWSDNWREILDSKR
Ligand information
Ligand IDO84
InChIInChI=1S/C19H22N2O11P2/c22-17-12(5-4-8-33(24,25)26)10-21(18(23)20-17)16-9-14-15(31-16)11-30-19(32-14,34(27,28)29)13-6-2-1-3-7-13/h1-7,10,14-16H,8-9,11H2,(H,20,22,23)(H2,24,25,26)(H2,27,28,29)/b5-4+/t14-,15-,16-,19-/m1/s1
InChIKeyTZXVMSWLUKAZDT-PDBOZARJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)[C@]2(OC[C@@H]3[C@H](O2)C[C@@H](O3)N4C=C(C(=O)NC4=O)/C=C/CP(=O)(O)O)P(=O)(O)O
CACTVS 3.385O[P](O)(=O)CC=CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
OpenEye OEToolkits 2.0.6c1ccc(cc1)C2(OCC3C(O2)CC(O3)N4C=C(C(=O)NC4=O)C=CCP(=O)(O)O)P(=O)(O)O
CACTVS 3.385O[P](O)(=O)C\C=C\C1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
FormulaC19 H22 N2 O11 P2
Name[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-[(~{E})-3-phosphonoprop-1-enyl]pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid
ChEMBL
DrugBank
ZINC
PDB chain6g2n Chain B Residue 302 [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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PDB6g2n Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases
Resolution1.4 Å
Binding residue
(original residue number in PDB)		D14 D16 F22 F48 L49 A50 Y69 S104 L106 L107 R136 K138
Binding residue
(residue number reindexed from 1)		D7 D9 F15 F41 L42 A43 Y62 S97 L99 L100 R129 K131
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.14,Ki=72.0nM
Enzymatic activity
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:6g2n, PDBe:6g2n, PDBj:6g2n
PDBsum6g2n
PubMed
UniProtQ8TCD5|NT5C_HUMAN 5'(3')-deoxyribonucleotidase, cytosolic type (Gene Name=NT5C)

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