Structure of PDB 3cd2 Chain A Binding Site BS02

Receptor Information
>3cd2 Chain A (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 IDMTX
InChIInChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1
InChIKeyFBOZXECLQNJBKD-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)nc(nc3N)N)CCC(=O)O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
FormulaC20 H22 N8 O5
NameMETHOTREXATE
ChEMBLCHEMBL34259
DrugBankDB00563
ZINCZINC000001529323
PDB chain3cd2 Chain A Residue 307 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3cd2 Ligand-induced conformational changes in the crystal structures of Pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		I10 L25 E32 I33 F36 F69 R75 I123
Binding residue
(residue number reindexed from 1)		I10 L25 E32 I33 F36 F69 R75 I123
Annotation score2
Binding affinityBindingDB: IC50=1nM,Ki=0.008000nM
Enzymatic activity
Catalytic site (original residue number in PDB) L25 E32
Catalytic site (residue number reindexed from 1) L25 E32
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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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3cd2, PDBe:3cd2, PDBj:3cd2
PDBsum3cd2
PubMed10194348
UniProtP16184|DYR_PNECA Dihydrofolate reductase

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