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Receptor Information

>6g2m Chain A (length=197) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SNARALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQ
YGRLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICT
SPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDI
TGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP

Ligand ID

O84

InChI

InChI=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

InChIKey

TZXVMSWLUKAZDT-PDBOZARJSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	c1ccc(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 3.385	O[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 2.0.6	c1ccc(cc1)C2(OCC3C(O2)CC(O3)N4C=C(C(=O)NC4=O)C=CCP(=O)(O)O)P(=O)(O)O
CACTVS 3.385	O[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

Formula

C19 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 chain

6g2m Chain A Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6g2m Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases
Resolution	1.37 Å
Binding residue (original residue number in PDB)	D41 D43 F49 F75 W76 V77 W96 S131 I133 K134 R163 K165
Binding residue (residue number reindexed from 1)	D11 D13 F19 F45 W46 V47 W66 S101 I103 K104 R133 K135
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=7.82,Ki=15.1nM

Catalytic site (original residue number in PDB)	D41 D43 D176
Catalytic site (residue number reindexed from 1)	D11 D13 D146
Enzyme Commision number	3.1.3.-

	Molecular Function
GO:0008253	5'-nucleotidase activity

	Biological Process
GO:0009264	deoxyribonucleotide catabolic process

PDB	RCSB:6g2m, PDBe:6g2m, PDBj:6g2m
PDBsum	6g2m
PubMed
UniProt	Q9NPB1\|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)

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Structure of PDB 6g2m Chain A Binding Site BS01