Structure of PDB 5km4 Chain A Binding Site BS01

Receptor Information
>5km4 Chain A (length=115) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPGGDTIFGKIIRKEIPAKIIFEDDRCLAFHDISPQAPTHFLVIPKKHIS
QISVAEDDDESLLGHLMIVGKKCAADLGLNKGYRMVVNEGSDGGQSVYHV
HLHVLGGRQMHWPPG
Ligand information
Ligand IDIU
InChIInChI=1S/C9H12IN2O9P/c10-3-1-12(9(16)11-7(3)15)8-6(14)5(13)4(21-8)2-20-22(17,18)19/h1,4-6,8,13-14H,2H2,(H,11,15,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1
InChIKeyHXJLWCWPONZYNP-UAKXSSHOSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04IC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(I)C(=O)NC2=O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(I)C(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)I
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)I
FormulaC9 H12 I N2 O9 P
Name5-IODOURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL1229560
DrugBank
ZINCZINC000013518175
PDB chain5km4 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5km4 A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		I18 D43 I44 N99 Q106 S107 V108 H112 H114
Binding residue
(residue number reindexed from 1)		I7 D32 I33 N88 Q95 S96 V97 H101 H103
Annotation score2
Enzymatic activity
Enzyme Commision number 3.4.22.-
3.9.1.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0005080 protein kinase C binding
GO:0005515 protein binding
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0016929 deSUMOylase activity
GO:0043530 adenosine 5'-monophosphoramidase activity
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0006508 proteolysis
GO:0006915 apoptotic process
GO:0007165 signal transduction
GO:0009154 purine ribonucleotide catabolic process
GO:0016926 protein desumoylation
GO:0050850 positive regulation of calcium-mediated signaling
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
Cellular Component
GO:0000118 histone deacetylase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5km4, PDBe:5km4, PDBj:5km4
PDBsum5km4
PubMed28968488
UniProtP49773|HINT1_HUMAN Adenosine 5'-monophosphoramidase HINT1 (Gene Name=HINT1)

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