Structure of PDB 5kma Chain A Binding Site BS01

Receptor Information
>5kma 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
NLHVLGGRQMHWPPG
Ligand information
Ligand ID777
InChIInChI=1S/C12H19N6O7P/c1-2-15-26(22,23)24-3-5-7(19)8(20)11(25-5)18-4-14-6-9(18)16-12(13)17-10(6)21/h4-5,7-8,11,19-20H,2-3H2,1H3,(H2,15,22,23)(H3,13,16,17,21)/t5-,7-,8-,11-/m1/s1
InChIKeyBTIPXEHUJHIGFX-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5CCNP(=O)(O)OCC1C(C(C(O1)n2cnc3c2NC(=NC3=O)N)O)O
OpenEye OEToolkits 2.0.5CCNP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2NC(=NC3=O)N)O)O
CACTVS 3.385CCN[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)N=C(N)Nc23
CACTVS 3.385CCN[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)N=C(N)Nc23
FormulaC12 H19 N6 O7 P
Name[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-ethyl-phosphonamidic acid;
D-Trp-G
ChEMBL
DrugBank
ZINC
PDB chain5kma Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5kma A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		I18 F41 D43 I44 N99 G105 S107 V108 N112 H114
Binding residue
(residue number reindexed from 1)		I7 F30 D32 I33 N88 G94 S96 V97 N101 H103
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=4.71,Kd=19.6uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5kma, PDBe:5kma, PDBj:5kma
PDBsum5kma
PubMed28968488
UniProtP49773|HINT1_HUMAN Adenosine 5'-monophosphoramidase HINT1 (Gene Name=HINT1)

[Back to BioLiP]