Structure of PDB 6prd Chain A Binding Site BS01

Receptor Information
>6prd Chain A (length=162) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESI
GKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEE
MIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHT
FLHLIRKKLVPR
Ligand information
Ligand IDOWG
InChIInChI=1S/C33H38N6O6/c1-41-24-9-6-20(7-10-24)30-25-16-27(43-3)26(42-2)15-22(25)18-37-39(30)29(40)11-8-21-12-19(14-28(44-4)31(21)45-5)13-23-17-36-33(35)38-32(23)34/h6-7,9-10,12,14-17,30,37H,8,11,13,18H2,1-5H3,(H4,34,35,36,38)/t30-/m0/s1
InChIKeyLGRHLMMHEUVVCK-PMERELPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(cc1)[CH]2N(NCc3cc(OC)c(OC)cc23)C(=O)CCc4cc(Cc5cnc(N)nc5N)cc(OC)c4OC
OpenEye OEToolkits 2.0.7COc1ccc(cc1)[C@H]2c3cc(c(cc3CNN2C(=O)CCc4cc(cc(c4OC)OC)Cc5cnc(nc5N)N)OC)OC
OpenEye OEToolkits 2.0.7COc1ccc(cc1)C2c3cc(c(cc3CNN2C(=O)CCc4cc(cc(c4OC)OC)Cc5cnc(nc5N)N)OC)OC
CACTVS 3.385COc1ccc(cc1)[C@@H]2N(NCc3cc(OC)c(OC)cc23)C(=O)CCc4cc(Cc5cnc(N)nc5N)cc(OC)c4OC
ACDLabs 12.01c5(c(CCC(N1C(c2c(CN1)cc(OC)c(OC)c2)c3ccc(cc3)OC)=O)cc(Cc4c(nc(N)nc4)N)cc5OC)OC
FormulaC33 H38 N6 O6
Name3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-6,7-dimethoxy-1-(4-methoxyphenyl)-3,4-dihydrophthalazin-2(1H)-yl]propan-1-one
ChEMBL
DrugBank
ZINC
PDB chain6prd Chain A Residue 403 [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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PDB6prd Inhibitor design to target a unique feature in the folate pocket of Staphylococcus aureus dihydrofolate reductase.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		L5 V6 A7 L20 D27 L28 K29 V31 K32 S49 L54 P55 R57 F92
Binding residue
(residue number reindexed from 1)		L5 V6 A7 L20 D27 L28 K29 V31 K32 S49 L54 P55 R57 F92
Annotation score1
Binding affinityMOAD: Ki=1nM
Enzymatic activity
Catalytic site (original residue number in PDB) L5 L20 W22 D27 L28 V31 L54 V89 T111
Catalytic site (residue number reindexed from 1) L5 L20 W22 D27 L28 V31 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:0046452 dihydrofolate metabolic process
GO:0046654 tetrahydrofolate biosynthetic process
GO:0046655 folic acid metabolic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6prd, PDBe:6prd, PDBj:6prd
PDBsum6prd
PubMed32502861
UniProtP0A017|DYR_STAAU Dihydrofolate reductase (Gene Name=folA)

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