Structure of PDB 6hdy Chain A Binding Site BS02

Receptor Information
>6hdy Chain A (length=474) Species: 391953 (Aquincola tertiaricarbonis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGMEEWNFPVEYDENYLPPADSRYWFPRRETMPAAERDKAILGRLQQVCQ
YAWEHAPFYRRKWEEAGFQPSQLKSLEDFEARVPVVKKTDLRESQAAHPP
FGDYVCVPNSEIFHVHGTSRPTAFGIGRADWRAIANAHARIMWGMGIRPG
DLVCVAAVFSLYMGSWGALAGAERLRAKAFPFGAGAPGMSARLVQWLDTM
KPAAFYGTPSYAIHLAEVAREEKLNPRNFGLKCLFFSGEPGASVPGVKDR
IEEAYGAKVYDCGSMAEMSPFMNVAGTEQSNDGMLCWQDIIYTEVCDPAN
MRRVPYGQRGTPVYTHLERTSQPMIRLLSGDLTLWTNDENPCGRTYPRLP
QGIFGRIDDMFTIRGENIYPSEIDAALNQMSGYGGEHRIVITRESAMDEL
LLRVEPSESVHAAGAAALETFRTEASHRVQTVLGVRAKVELVAPNSIART
DFKARRVIDDREVFRALNQQLQSS
Ligand information
Ligand ID8LQ
InChIInChI=1S/C14H20N5O9P/c1-6(20)2-8(21)28-29(24,25)26-3-7-10(22)11(23)14(27-7)19-5-18-9-12(15)16-4-17-13(9)19/h4-7,10-11,14,20,22-23H,2-3H2,1H3,(H,24,25)(H2,15,16,17)/t6-,7+,10+,11+,14+/m0/s1
InChIKeyZNHASVNGLACCHV-LTOLZBHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H](O)CC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
CACTVS 3.385C[CH](O)CC(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.6CC(CC(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)O
OpenEye OEToolkits 2.0.6C[C@@H](CC(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)O
FormulaC14 H20 N5 O9 P
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (3~{S})-3-oxidanylbutanoate
ChEMBL
DrugBank
ZINC
PDB chain6hdy Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6hdy Structures of 2-Hydroxyisobutyric Acid-CoA Ligase Reveal Determinants of Substrate Specificity and Describe a Multi-Conformational Catalytic Cycle.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Y164 G166 S239 G240 E241 P242 C264 G265 S266 A268 F273 D333 I355 R358 K455
Binding residue
(residue number reindexed from 1)		Y162 G164 S237 G238 E239 P240 C262 G263 S264 A266 F271 D331 I353 R356 K453
Annotation score1
Enzymatic activity
Enzyme Commision number 6.2.1.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016874 ligase activity

View graph for
Molecular Function
External links
PDB RCSB:6hdy, PDBe:6hdy, PDBj:6hdy
PDBsum6hdy
PubMed31145912
UniProtI3VE75

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