Structure of PDB 3nz9 Chain X Binding Site BS02

Receptor Information
>3nz9 Chain X (length=206) Species: 4754 (Pneumocystis carinii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNQQKSLTLIVALTTSYGIGRSNSLPWKLKKEISYFKRVTSFVPTFDSFE
SMNVVLMGRKTWESIPLQFRPLKGRINVVITRNESLDLGNGIHSAKSLDH
ALELLYRTYGSESSVQINRIFVIGGAQLYKAAMDHPKLDRIMATIIYKDI
HCDVFFPLKFRDKEWSSVWKKEKHSDLESWVGTKVPHGKINEDGFDYEFE
MWTRDL
Ligand information
Ligand IDD2K
InChIInChI=1S/C22H27N5O4/c1-4-30-18(28)6-5-9-31-16-7-8-17(29-3)14(11-16)10-15-12-25-21-19(13(15)2)20(23)26-22(24)27-21/h7-8,11-12H,4-6,9-10H2,1-3H3,(H4,23,24,25,26,27)
InChIKeyOJXNTDHQQMJPKJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCOC(=O)CCCOc1ccc(c(c1)Cc2cnc3c(c2C)c(nc(n3)N)N)OC
ACDLabs 12.01O=C(OCC)CCCOc1cc(c(OC)cc1)Cc2c(c3c(nc2)nc(nc3N)N)C
CACTVS 3.370CCOC(=O)CCCOc1ccc(OC)c(Cc2cnc3nc(N)nc(N)c3c2C)c1
FormulaC22 H27 N5 O4
Nameethyl 4-{3-[(2,4-diamino-5-methylpyrido[2,3-d]pyrimidin-6-yl)methyl]-4-methoxyphenoxy}butanoate
ChEMBLCHEMBL189796
DrugBank
ZINCZINC000013646394
PDB chain3nz9 Chain X Residue 207 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nz9 Structural analysis of Pneumocystis carinii and human DHFR complexes with NADPH and a series of five potent 6-[5'-([omega]-carboxyalkoxy)benzyl]pyrido[2,3-d]pyrimidine derivatives
Resolution1.8 Å
Binding residue
(original residue number in PDB)		I10 V11 A12 L25 E32 I33 F36 P66 F69 I123
Binding residue
(residue number reindexed from 1)		I10 V11 A12 L25 E32 I33 F36 P66 F69 I123
Annotation score1
Binding affinityMOAD: ic50=6.5nM
BindingDB: IC50=6.5nM
Enzymatic activity
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:0005739 mitochondrion

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Cellular Component
External links
PDB RCSB:3nz9, PDBe:3nz9, PDBj:3nz9
PDBsum3nz9
PubMed21206056
UniProtP16184|DYR_PNECA Dihydrofolate reductase

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