Structure of PDB 3dfr Chain A Binding Site BS01

Receptor Information
>3dfr Chain A (length=162) Species: 1582 (Lacticaseibacillus casei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TAFLWAQNRNGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESFP
KRPLPERTNVVLTHQEDYQAQGAVVVHDVAAVFAYAKQHLDQELVIAGGA
QIFTAFKDDVDTLLVTRLAGSFEGDTKMIPLNWDDFTKVSSRTVEDTNPA
LTHTYEVWQKKA
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain3dfr Chain A Residue 163 [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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PDB3dfr Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		W5 A6 I13 G17 H18 L19 G42 R43 R44 T45 L62 T63 H64 Q65 A97 G99 A100 Q101 I102
Binding residue
(residue number reindexed from 1)		W5 A6 I13 G17 H18 L19 G42 R43 R44 T45 L62 T63 H64 Q65 A97 G99 A100 Q101 I102
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) L4 L19 W21 D26 L27 F30 L54 L94 T116
Catalytic site (residue number reindexed from 1) L4 L19 W21 D26 L27 F30 L54 L94 T116
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:0031427 response to methotrexate
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dfr, PDBe:3dfr, PDBj:3dfr
PDBsum3dfr
PubMed6815178
UniProtP00381|DYR_LACCA Dihydrofolate reductase (Gene Name=folA)

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