Structure of PDB 4yca Chain A Binding Site BS01

Receptor Information
>4yca Chain A (length=284) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSVAIIGPGAVGTTIAYELQQSLPHTTLIGRHAKTITYYTVPHAPAQDIV
VKGYEDVTNTFDVIIIAVKTHQLDAVIPHLTYLAHEDTLIILAQNGYLEH
IPFKNVCQAVVYISGQKKGDVVTHFRDYQLRIQDNALTRQFRDLVQDSQI
DIVLEANIQQAIWYKLLVNLGINSITALGRQTVAIMHNPEIRILCRQLLL
DGCRVAQAEGLNFSEQTVDTIMTIYQGYPDEMGTSMYYDIVHQQPLEVEA
IQGFIYRRAREHNLDTPYLDTIYSFLRAYQQNEG
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain4yca Chain A Residue 800 [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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PDB4yca Evidence of Kinetic Cooperativity in Dimeric Ketopantoate Reductase from Staphylococcus aureus.
Resolution1.81 Å
Binding residue
(original residue number in PDB)		P10 G11 A12 V13 R33 Y56 V70 Q74 Q96 N97 V115 I117 S118 G119 K121 E251
Binding residue
(residue number reindexed from 1)		P8 G9 A10 V11 R31 Y54 V68 Q72 Q94 N95 V111 I113 S114 G115 K117 E247
Annotation score4
Binding affinityMOAD: Kd=117nM
Enzymatic activity
Catalytic site (original residue number in PDB) K169
Catalytic site (residue number reindexed from 1) K165
Enzyme Commision number 1.1.1.169: 2-dehydropantoate 2-reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004616 phosphogluconate dehydrogenase (decarboxylating) activity
GO:0008677 2-dehydropantoate 2-reductase activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0015940 pantothenate biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4yca, PDBe:4yca, PDBj:4yca
PDBsum4yca
PubMed25946571
UniProtA0A0J9X283

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