Structure of PDB 2w9s Chain B Binding Site BS01

Receptor Information
>2w9s Chain B (length=157) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLSIIVAHDKQRVIGYQNQLPWHLPNDLKHIKQLTTGNTLVMARKTFESI
GKPLPNRRNVVLTNQASFHHEGVDVINSLDEIKELSGHVFIFGGQTLYEA
MIDQVDDMYITVIDGKFQGDTFFPPYTFEDWEVESSVEGQLDEKNTIPHT
FLHLVRR
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 chain2w9s Chain B Residue 1159 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2w9s Structural Comparison of Chromosomal and Exogenous Dihydrofolate Reductase from Staphylococcus Aureus in Complex with the Potent Inhibitor Trimethoprim.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		V6 A7 I14 N18 Q19 L20 A43 R44 K45 T46 L62 T63 N64 Q65 N77 F92 G94 Q95 T96
Binding residue
(residue number reindexed from 1)		V6 A7 I14 N18 Q19 L20 A43 R44 K45 T46 L62 T63 N64 Q65 N77 F92 G94 Q95 T96
Annotation score4
Binding affinityMOAD: Kd=2370nM
Enzymatic activity
Catalytic site (original residue number in PDB) I5 L20 W22 D27 L28 I31 L54 V89 T111
Catalytic site (residue number reindexed from 1) I5 L20 W22 D27 L28 I31 L54 V89 T111
Enzyme Commision number 1.5.1.3: dihydrofolate reductase.
Gene Ontology
Molecular Function
GO:0004146 dihydrofolate reductase activity
GO:0016491 oxidoreductase activity
GO:0050661 NADP binding
Biological Process
GO:0006730 one-carbon metabolic process
GO:0031427 response to methotrexate
GO:0046452 dihydrofolate metabolic process
GO:0046654 tetrahydrofolate biosynthetic process
GO:0046655 folic acid metabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2w9s, PDBe:2w9s, PDBj:2w9s
PDBsum2w9s
PubMed19280600
UniProtP13955|DYRA_STAAU Dihydrofolate reductase type 1 from Tn4003 (Gene Name=dfrA)

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