Structure of PDB 5nx9 Chain A Binding Site BS04

Receptor Information
>5nx9 Chain A (length=466) Species: 63221 (Homo sapiens neanderthalensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPDSYRSPLASRYASPEMCFVFSDRYKFRTWRQLWLWLAEAEQTLGLPIT
DEQIQEMKSNLENIDFKMAAEEEKRLRHDVMAHVHTFGHCCPKAAGIIHL
GATSCYVGDNTDLIILRNALDLLLPKLARVISRLADFAKERASLPTLGFT
HFQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDDLRFRGVKGTTGTQASF
LQLFEGDDHKVEQLDKMVTEKAGFKRAFIITGQTYTRKVDIEVLSVLASL
GASVHKICTDIRLLANLKEMEEPFEKQQIGKRNPMRSERCCSLARHLMTL
VMDPLQTASVQWFERTLDDSANRRICLAEAFLTADTILNTLQNISEGLVV
YPKVIERRIRQELPFMATENIIMAMVKAGGSRQDCHEKIRVLSQQAASVV
KQEGGDNDLIERIQADAYFSPIHSQLDHLLDPSSFTGRASQQVQRFLEEE
VYPLLKPYESVMKVKA
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain5nx9 Chain D Residue 502 [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]
PDB5nx9 Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R20 Y21 R303
Binding residue
(residue number reindexed from 1)		R12 Y13 R289
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=4.60,Kd~25uM
Enzymatic activity
Catalytic site (original residue number in PDB) H86 T158 H159 K295 E302
Catalytic site (residue number reindexed from 1) H78 T150 H151 K281 E288
Enzyme Commision number 4.3.2.2: adenylosuccinate lyase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity
GO:0016829 lyase activity
GO:0070626 (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity
Biological Process
GO:0006164 purine nucleotide biosynthetic process
GO:0006189 'de novo' IMP biosynthetic process
GO:0009152 purine ribonucleotide biosynthetic process
GO:0009168 purine ribonucleoside monophosphate biosynthetic process
GO:0044208 'de novo' AMP biosynthetic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5nx9, PDBe:5nx9, PDBj:5nx9
PDBsum5nx9
PubMed30573755
UniProtA0A384E0N4

[Back to BioLiP]