Structure of PDB 5nxa Chain D Binding Site BS03

Receptor Information
>5nxa Chain D (length=440) Species: 63221 (Homo sapiens neanderthalensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSPDSYRSPLASRYASPEMCFVFSDRYKFRTWRQLWLWLAEAEQTLGLPI
TDEQIQEMKSNLENIDFKMAAEEEKRLRHDVMAHVHTFGHCCPKAAGIIH
LGATSCYVGDNTDLIILRNALDLLLPKLARVISRLADFAKERASLPTLGF
THFQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDDLRFRGVKGTTGTQAS
FLQLFEGDDHKVEQLDKMVTEKAGFKRAFIITGQTYTRKVDIEVLSVLAS
LGASVHKICTDIRLLANLKEMEEPFEKQQKRNPMRSERCCSLARHLMTLV
MDPLQTASVQWFERTLDDSANRRICLAEAFLTADTILNTLQNISEGLVVY
PKVIERRIRQELPFMATENIIDCHEKIRVLSQQAASVVKQEGGDNDLIER
DPSSFTGRASQQVQRFLEEEVYPLLKPYESVMKVKAELCL
Ligand information
Ligand IDSSS
InChIInChI=1S/C13H19N4O12P/c14-10-7(11(22)16-4(13(23)24)1-6(18)19)15-3-17(10)12-9(21)8(20)5(29-12)2-28-30(25,26)27/h3-5,8-9,12,20-21H,1-2,14H2,(H,16,22)(H,18,19)(H,23,24)(H2,25,26,27)/t4-,5+,8+,9-,12+/m0/s1
InChIKeyNAQGHJTUZRHGAC-PSYSQGJASA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1n(cnc1C(=O)N[CH](CC(O)=O)C(O)=O)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
CACTVS 3.341Nc1n(cnc1C(=O)N[C@@H](CC(O)=O)C(O)=O)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]2O
OpenEye OEToolkits 1.5.0c1nc(c(n1[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)C(=O)N[C@@H](CC(=O)O)C(=O)O
ACDLabs 10.04O=C(O)CC(C(=O)O)NC(=O)c1ncn(c1N)C2OC(C(O)C2O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc(c(n1C2C(C(C(O2)COP(=O)(O)O)O)O)N)C(=O)NC(CC(=O)O)C(=O)O
FormulaC13 H19 N4 O12 P
NameN-{[5-AMINO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZOL-4-YL]CARBONYL}-L-ASPARTIC ACID;
N-{[5-AMINO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZOL-4-YL]CARBONYL}-L-ASPARTIC ACID
ChEMBL
DrugBank
ZINCZINC000038191900
PDB chain5nxa Chain D Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nxa Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R85 H86 D87 T111 S112 Q241 L331 S334 A335 R338
Binding residue
(residue number reindexed from 1)		R78 H79 D80 T104 S105 Q234 L316 S319 A320 R323
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H86 T158 H159 K295 E302
Catalytic site (residue number reindexed from 1) H79 T151 H152 K280 E287
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nxa, PDBe:5nxa, PDBj:5nxa
PDBsum5nxa
PubMed30573755
UniProtA0A384E0N4

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