Structure of PDB 1kmv Chain A Binding Site BS01

Receptor Information
>1kmv Chain A (length=185) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLV
IMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLT
EQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPE
IDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKN
Ligand information
Ligand IDLII
InChIInChI=1S/C18H19N5O2/c1-10-12(9-21-17-15(10)16(19)22-18(20)23-17)5-4-11-8-13(24-2)6-7-14(11)25-3/h4-9H,1-3H3,(H4,19,20,21,22,23)/b5-4-
InChIKeyWNDJHUNKXPAREB-PLNGDYQASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(cnc2c1c(nc(n2)N)N)\C=C/c3cc(ccc3OC)OC
ACDLabs 10.04n1cc(c(c2c1nc(nc2N)N)C)/C=C\c3cc(OC)ccc3OC
OpenEye OEToolkits 1.5.0Cc1c(cnc2c1c(nc(n2)N)N)C=Cc3cc(ccc3OC)OC
CACTVS 3.341COc1ccc(OC)c(C=Cc2cnc3nc(N)nc(N)c3c2C)c1
CACTVS 3.341COc1ccc(OC)c(\C=C/c2cnc3nc(N)nc(N)c3c2C)c1
FormulaC18 H19 N5 O2
Name(Z)-6-(2-[2,5-DIMETHOXYPHENYL]ETHEN-1-YL)-2,4-DIAMINO-5-METHYLPYRIDO[2,3-D]PYRIMIDINE;
SRI-9662
ChEMBL
DrugBankDB03060
ZINCZINC000005891398
PDB chain1kmv Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1kmv Atomic structures of human dihydrofolate reductase complexed with NADPH and two lipophilic antifolates at 1.09 a and 1.05 a resolution.
Resolution1.05 Å
Binding residue
(original residue number in PDB)		I7 V8 E30 F31 F34 P61 V115
Binding residue
(residue number reindexed from 1)		I7 V8 E30 F31 F34 P61 V115
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.95,IC50=112nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kmv, PDBe:1kmv, PDBj:1kmv
PDBsum1kmv
PubMed12096917
UniProtP00374|DYR_HUMAN Dihydrofolate reductase (Gene Name=DHFR)

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