Structure of PDB 3ix9 Chain B Binding Site BS02

Receptor Information
>3ix9 Chain B (length=166) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKKIVAIWAQDEEGVIGKDNRLPWYLPAELQHFKETTLNHAILMGRVTFD
GMGRRLLPKRETLILTRNPEEKIDGVATFHDVQSVLDWYSAQEKNLYIVG
GKQIFQAFEPYLDEVIVTHIHARVEGDTYFPAEFDLSLFETVSSKFYTKD
EKNPYDFTIQYRKRKE
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 chain3ix9 Chain B Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3ix9 Kinetic and structural characterization of dihydrofolate reductase from Streptococcus pneumoniae
Resolution1.95 Å
Binding residue
(original residue number in PDB)		I8 W9 L23 E30 L31 Q32 F34 K35 L58 R61 V100
Binding residue
(residue number reindexed from 1)		I7 W8 L22 E29 L30 Q31 F33 K34 L57 R60 V99
Annotation score2
Binding affinityMOAD: Ki=3.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) I8 L23 W25 E30 L31 F34 L58 L97 T119
Catalytic site (residue number reindexed from 1) I7 L22 W24 E29 L30 F33 L57 L96 T118
Enzyme Commision number 1.5.1.3: dihydrofolate reductase.
Gene Ontology
Molecular Function
GO:0004146 dihydrofolate reductase activity
GO:0005515 protein binding
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
GO:0046677 response to antibiotic
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ix9, PDBe:3ix9, PDBj:3ix9
PDBsum3ix9
PubMed19950924
UniProtQ54801|DYR_STRPN Dihydrofolate reductase (Gene Name=dhfR)

[Back to BioLiP]