Structure of PDB 1pd9 Chain A Binding Site BS01

Receptor Information
>1pd9 Chain A (length=186) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLV
IMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLT
EQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPE
IDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
Ligand information
Ligand IDCO4
InChIInChI=1S/C19H24N6O3/c1-10-11(8-22-18-15(10)17(20)23-19(21)24-18)9-25(2)12-6-13(26-3)16(28-5)14(7-12)27-4/h6-8H,9H2,1-5H3,(H4,20,21,22,23,24)
InChIKeyPEGMMEYCSOZKIT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04n1cc(c(c2c1nc(nc2N)N)C)CN(c3cc(OC)c(OC)c(OC)c3)C
CACTVS 3.341COc1cc(cc(OC)c1OC)N(C)Cc2cnc3nc(N)nc(N)c3c2C
OpenEye OEToolkits 1.5.0Cc1c(cnc2c1c(nc(n2)N)N)C[N@@](C)c3cc(c(c(c3)OC)OC)OC
OpenEye OEToolkits 1.5.0Cc1c(cnc2c1c(nc(n2)N)N)CN(C)c3cc(c(c(c3)OC)OC)OC
FormulaC19 H24 N6 O3
Name2,4-DIAMINO-5-METHYL-6-[(3,4,5-TRIMETHOXY-N-METHYLANILINO)METHYL]PYRIDO[2,3-D]PYRIMIDINE
ChEMBLCHEMBL50514
DrugBankDB02104
ZINCZINC000012501589
PDB chain1pd9 Chain A Residue 187 [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]
PDB1pd9 Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		I7 V8 E30 F31 F34 P61 N64 V115
Binding residue
(residue number reindexed from 1)		I7 V8 E30 F31 F34 P61 N64 V115
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) L22 E30
Catalytic site (residue number reindexed from 1) L22 E30
Enzyme Commision number 1.5.1.3: dihydrofolate reductase.
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0004146 dihydrofolate reductase activity
GO:0005542 folic acid binding
GO:0016491 oxidoreductase activity
GO:0050661 NADP binding
GO:0070402 NADPH binding
GO:1990825 sequence-specific mRNA binding
Biological Process
GO:0006729 tetrahydrobiopterin biosynthetic process
GO:0006730 one-carbon metabolic process
GO:0017148 negative regulation of translation
GO:0031103 axon regeneration
GO:0031427 response to methotrexate
GO:0046452 dihydrofolate metabolic process
GO:0046653 tetrahydrofolate metabolic process
GO:0046654 tetrahydrofolate biosynthetic process
GO:0046655 folic acid metabolic process
GO:0051000 positive regulation of nitric-oxide synthase activity
GO:2000121 regulation of removal of superoxide radicals
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1pd9, PDBe:1pd9, PDBj:1pd9
PDBsum1pd9
PubMed12925791
UniProtP00374|DYR_HUMAN Dihydrofolate reductase (Gene Name=DHFR)

[Back to BioLiP]