Structure of PDB 6pcd Chain D Binding Site BS01

Receptor Information
>6pcd Chain D (length=402) Species: 160488 (Pseudomonas putida KT2440) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSMHDVFICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNPGVQWDQ
VDEVFFGCANQAGEDNRNVARMALLLAGLPESIPGVTLNRLSASGMDAVG
TAFRAIASGEMELVIAGGVESMSRAPFVMGKAESAYSRNMKLEDTTIGWR
FINPLMKSQYGVDSMPETADNVADDYQVSRADQDAFALRSQQKAAAAQAA
GFFAEEIVPVRIAHKKGEIIVERDEHLRPETTLEALTKLKPVNGPDKTVT
AGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGP
VPAVRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPN
GGAIALGAPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIE
RV
Ligand information
Ligand IDCOA
InChIInChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
InChIKeyRGJOEKWQDUBAIZ-IBOSZNHHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
ACDLabs 10.04O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC21 H36 N7 O16 P3 S
NameCOENZYME A
ChEMBLCHEMBL1213327
DrugBankDB01992
ZINCZINC000008551087
PDB chain6pcd Chain D Residue 501 [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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PDB6pcd Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase.
Resolution1.37 Å
Binding residue
(original residue number in PDB)		I145 M163 R226 T229 A249 S253 G254 N322 A324 A356
Binding residue
(residue number reindexed from 1)		I147 M165 R228 T231 A251 S255 G256 N324 A326 A358
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) S90 A356 C386 G388
Catalytic site (residue number reindexed from 1) S92 A358 C388 G390
Enzyme Commision number 2.3.1.174: 3-oxoadipyl-CoA thiolase.
Gene Ontology
Molecular Function
GO:0003988 acetyl-CoA C-acyltransferase activity
GO:0016746 acyltransferase activity
GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
GO:0033812 3-oxoadipyl-CoA thiolase activity
Biological Process
GO:0006635 fatty acid beta-oxidation
GO:0010124 phenylacetate catabolic process
GO:0019619 3,4-dihydroxybenzoate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6pcd, PDBe:6pcd, PDBj:6pcd
PDBsum6pcd
PubMed32647822
UniProtQ88N39

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