Structure of PDB 3wdm Chain D Binding Site BS01

Receptor Information
>3wdm Chain D (length=255) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNIPKSHPRYWSLYYREKIIEGMEKGMTAKAGLIAHGRGEAFDYLIGERT
IEPAERAMRAAVAKFLLAEHPVISVNGNVAALVPKETIELAKALNAKLEI
NLFYRTEERVRTIAEELRKYDPEIEILGINPTKRIPGLEGKVDENGIWKA
DVVLVPLEDGDRTEALVRMGKFVVTVDLNPLSRSARMADITIVDNIVRAY
PRMVELAREMKDYSREELLKIVGEYDNGKTLSDVLLHIRDRLTRLAEEGI
WRRKE
Ligand information
Ligand IDADN
InChIInChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
InChIKeyOIRDTQYFTABQOQ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
FormulaC10 H13 N5 O4
NameADENOSINE
ChEMBLCHEMBL477
DrugBankDB00640
ZINCZINC000002169830
PDB chain3wdm Chain D Residue 301 [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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PDB3wdm Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis
Resolution2.0 Å
Binding residue
(original residue number in PDB)		A36 R39 L161 D181 L182 N183 N199 I200
Binding residue
(residue number reindexed from 1)		A35 R38 L157 D177 L178 N179 N195 I196
Annotation score3
Enzymatic activity
Enzyme Commision number 6.3.2.36: 4-phosphopantoate--beta-alanine ligase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
Biological Process
GO:0015937 coenzyme A biosynthetic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:3wdm, PDBe:3wdm, PDBj:3wdm
PDBsum3wdm
PubMed24638914
UniProtQ5JIZ8|PPS_THEKO 4-phosphopantoate--beta-alanine ligase (Gene Name=TK1686)

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