Structure of PDB 3fra Chain X Binding Site BS02

Receptor Information
>3fra Chain X (length=157) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESI
GKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLYEE
MIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHT
FLHLIRK
Ligand information
Ligand IDI2H
InChIInChI=1S/C19H22N4O3/c1-24-15-8-11(7-12-9-22-19(21)23-18(12)20)13-5-6-14(10-3-4-10)26-16(13)17(15)25-2/h5-6,8-10,14H,3-4,7H2,1-2H3,(H4,20,21,22,23)/t14-/m1/s1
InChIKeyHWJPWWYTGBZDEG-CQSZACIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1cc(Cc2cnc(N)nc2N)c3C=C[CH](Oc3c1OC)C4CC4
ACDLabs 12.01n1cc(c(nc1N)N)Cc3cc(OC)c(OC)c2OC(C=Cc23)C4CC4
OpenEye OEToolkits 1.7.6COc1cc(c2c(c1OC)OC(C=C2)C3CC3)Cc4cnc(nc4N)N
OpenEye OEToolkits 1.7.6COc1cc(c2c(c1OC)O[C@H](C=C2)C3CC3)Cc4cnc(nc4N)N
CACTVS 3.385COc1cc(Cc2cnc(N)nc2N)c3C=C[C@@H](Oc3c1OC)C4CC4
FormulaC19 H22 N4 O3
Name5-{[(2S)-2-cyclopropyl-7,8-dimethoxy-2H-chromen-5-yl]methyl}pyrimidine-2,4-diamine
ChEMBLCHEMBL1673303
DrugBankDB07938
ZINCZINC000001486728
PDB chain3fra Chain X Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3fra Increased hydrophobic interactions of iclaprim with Staphylococcus aureus dihydrofolate reductase are responsible for the increase in affinity and antibacterial activity
Resolution2.35 Å
Binding residue
(original residue number in PDB)		L5 V6 A7 L20 D27 L28 V31 S49 F92
Binding residue
(residue number reindexed from 1)		L5 V6 A7 L20 D27 L28 V31 S49 F92
Annotation score1
Binding affinityMOAD: Ka=76000000M^-1
BindingDB: IC50=2.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) L5
Catalytic site (residue number reindexed from 1) L5
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3fra, PDBe:3fra, PDBj:3fra
PDBsum3fra
PubMed19211577
UniProtP0A017|DYR_STAAU Dihydrofolate reductase (Gene Name=folA)

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