Structure of PDB 1d6h Chain A Binding Site BS01

Receptor Information
>1d6h Chain A (length=387) Species: 3879 (Medicago sativa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVSEIRKAQRAEGPATILAIGTANPANCVEQSTYPDFYFKITNSEHKTEL
KEKFQRMCDKSMIKRRYMYLTEEILKENPNVCEYMAPSLDARQDMVVVEV
PRLGKEAAVKAIKEWGQPKSKITHLIVCTTSGVDMPGADYQLTKLLGLRP
YVKRYMMYQQGCFAGGTVLRLAKDLAENNKGARVLVVCSEVTAVTFRGPS
DTHLDSLVGQALFGDGAAALIVGSDPVPEIEKPIFEMVWTAQTIAPDSEG
AIDGHLREAGLTFHLLKDVPGIVSKNITKALVEAFEPLGISDYNSIFWIA
HPGGPAILDQVEQKLALKPEKMNATREVLSEYGAMSSACVLFILDEMRKK
STQNGLKTTGEGLEWGVLFGFGPGLTIETVVLRSVAI
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 chain1d6h Chain A Residue 390 [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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PDB1d6h Dissection of malonyl-coenzyme A decarboxylation from polyketide formation in the reaction mechanism of a plant polyketide synthase.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		K55 R58 M59 K62 L206 V271 P272 G306 P307 A308
Binding residue
(residue number reindexed from 1)		K53 R56 M57 K60 L204 V269 P270 G304 P305 A306
Annotation score3
Binding affinityMOAD: Kd=128nM
Enzymatic activity
Catalytic site (original residue number in PDB) C164 F215 H303 A336
Catalytic site (residue number reindexed from 1) C162 F213 H301 A334
Enzyme Commision number 2.3.1.74: chalcone synthase.
Gene Ontology
Molecular Function
GO:0016210 naringenin-chalcone synthase activity
GO:0016746 acyltransferase activity
GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
Biological Process
GO:0009058 biosynthetic process
GO:0009715 chalcone biosynthetic process
GO:0009813 flavonoid biosynthetic process
GO:0030639 polyketide biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1d6h, PDBe:1d6h, PDBj:1d6h
PDBsum1d6h
PubMed10653632
UniProtP30074|CHS2_MEDSA Chalcone synthase 2 (Gene Name=CHS2)

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