Structure of PDB 1ndz Chain A Binding Site BS02

Receptor Information
>1ndz Chain A (length=349) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPAFDKPKVELHVHLDGAIKPETILYYGKRRGIALPADTPEELQNIIGMD
KPLTLPDFLAKFDYYMPAIAGCRDAIKRIAYEFVEMKAKDGVVYVEVRYS
PHLLANSKVEPIPWNQAEGDLTPDEVVSLVNQGLQEGERDFGVKVRSILC
CMRHQPSWSSEVVELCKKYREQTVVAIDLAGDETIEGSSLFPGHVQAYAE
AVKSGVHRTVHAGEVGSANVVKEAVDTLKTERLGHGYHTLEDTTLYNRLR
QENMHFEICPWSSYLTGAWKPDTEHAVIRFKNDQVNYSLNTDDPLIFKST
LDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEDEKKELLDLLYKAYR
Ligand information
Ligand IDFR5
InChIInChI=1S/C27H29N7O3/c1-32-23-5-3-2-4-21(23)31-25(32)8-9-26(36)30-19-7-6-18-10-12-33(24(18)14-19)13-11-20(16-35)34-15-22(27(28)37)29-17-34/h2-7,10,12,14-15,17,20,35H,8-9,11,13,16H2,1H3,(H2,28,37)(H,30,36)/t20-/m1/s1
InChIKeyMBHAURHGCAJBCN-HXUWFJFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cn1c(CCC(=O)Nc2ccc3ccn(CC[CH](CO)n4cnc(c4)C(N)=O)c3c2)nc5ccccc15
OpenEye OEToolkits 1.5.0Cn1c2ccccc2nc1CCC(=O)Nc3ccc4ccn(c4c3)CCC(CO)n5cc(nc5)C(=O)N
CACTVS 3.341Cn1c(CCC(=O)Nc2ccc3ccn(CC[C@H](CO)n4cnc(c4)C(N)=O)c3c2)nc5ccccc15
OpenEye OEToolkits 1.5.0Cn1c2ccccc2nc1CCC(=O)Nc3ccc4ccn(c4c3)CC[C@H](CO)n5cc(nc5)C(=O)N
ACDLabs 10.04O=C(N)c1ncn(c1)C(CO)CCn3c2cc(ccc2cc3)NC(=O)CCc4nc5ccccc5n4C
FormulaC27 H29 N7 O3
Name1-((1R)-1-(HYDROXYMETHYL)-3-(6-((3-(1-METHYL-1H-BENZIMIDAZOL-2-YL)PROPANOYL)AMINO)-1H-INDOL-1-YL)PROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE;
FR235999
ChEMBLCHEMBL93280
DrugBank
ZINCZINC000002047652
PDB chain1ndz Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ndz A highly potent non-nucleoside adenosine deaminase inhibitor: efficient drug discovery by intentional lead hybridization
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H17 D19 F61 L62 F65 M155 G184 D185 T269 D296
Binding residue
(residue number reindexed from 1)		H14 D16 F58 L59 F62 M152 G181 D182 T266 D293
Annotation score1
Binding affinityMOAD: Ki=7.7nM
PDBbind-CN: -logKd/Ki=8.11,Ki=7.7nM
Enzymatic activity
Catalytic site (original residue number in PDB) H15 H17 H214 E217 H238 D295
Catalytic site (residue number reindexed from 1) H12 H14 H211 E214 H235 D292
Enzyme Commision number 3.5.4.4: adenosine deaminase.
Gene Ontology
Molecular Function
GO:0004000 adenosine deaminase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0019239 deaminase activity
GO:0046872 metal ion binding
GO:0046936 2'-deoxyadenosine deaminase activity
Biological Process
GO:0006154 adenosine catabolic process
GO:0007155 cell adhesion
GO:0009117 nucleotide metabolic process
GO:0009168 purine ribonucleoside monophosphate biosynthetic process
GO:0042110 T cell activation
GO:0043103 hypoxanthine salvage
GO:0046103 inosine biosynthetic process
GO:0060169 negative regulation of adenosine receptor signaling pathway
Cellular Component
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0031410 cytoplasmic vesicle
GO:0060205 cytoplasmic vesicle lumen
GO:0070161 anchoring junction

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ndz, PDBe:1ndz, PDBj:1ndz
PDBsum1ndz
PubMed14709046
UniProtP56658|ADA_BOVIN Adenosine deaminase (Gene Name=ADA)

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