Structure of PDB 7kdr Chain A Binding Site BS01

Receptor Information
>7kdr Chain A (length=158) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQ
PDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIML
FGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTR
AFDKLNKW
Ligand information
Ligand IDJ1L
InChIInChI=1S/C27H36N12O9S/c1-27(2)18(34-15-20(37-27)35-26(29)36-22(15)42)23(43)30-4-6-38-5-3-11(7-12(38)25(44)45)49(46,47)8-13-16(40)17(41)24(48-13)39-10-33-14-19(28)31-9-32-21(14)39/h9-13,16-17,24,40-41H,3-8H2,1-2H3,(H,30,43)(H,44,45)(H2,28,31,32)(H4,29,35,36,37,42)/t11-,12-,13-,16-,17-,24-/m1/s1
InChIKeyLIEKVCRXNQELKW-NERDUYAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1(C)NC2=C(N=C1C(=O)NCCN3CC[C@H](C[C@@H]3C(O)=O)[S](=O)(=O)C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)C(=O)NC(=N2)N
OpenEye OEToolkits 2.0.7CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCCN3CCC(CC3C(=O)O)S(=O)(=O)CC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)C
CACTVS 3.385CC1(C)NC2=C(N=C1C(=O)NCCN3CC[CH](C[CH]3C(O)=O)[S](=O)(=O)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)C(=O)NC(=N2)N
ACDLabs 12.01C(O)(C4CC(S(CC1C(O)C(C(O1)n2cnc3c2ncnc3N)O)(=O)=O)CCN4CCNC(C=6C(C)(C)NC=5N=C(NC(C=5N=6)=O)N)=O)=O
OpenEye OEToolkits 2.0.7CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCCN3CC[C@H](C[C@@H]3C(=O)O)S(=O)(=O)C[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)C
FormulaC27 H36 N12 O9 S
Name5'-{[(2R,4R)-1-{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}-2-carboxypiperidin-4-yl]sulfonyl}-5'-deoxyadenosine
ChEMBLCHEMBL4780649
DrugBank
ZINC
PDB chain7kdr 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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PDB7kdr Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Transition state analogs for high affinity binding.
Resolution1.488 Å
Binding residue
(original residue number in PDB)		P43 L45 Y53 N55 Q74 W89 R92 D95 D97 I98 R110 L111 T112 H115 Y116 F123
Binding residue
(residue number reindexed from 1)		P43 L45 Y53 N55 Q74 W89 R92 D95 D97 I98 R110 L111 T112 H115 Y116 F123
Annotation score1
Binding affinityMOAD: Kd=0.047uM
Enzymatic activity
Enzyme Commision number 2.7.6.3: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003848 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
Biological Process
GO:0009396 folic acid-containing compound biosynthetic process
GO:0016310 phosphorylation
GO:0046654 tetrahydrofolate biosynthetic process
GO:0046656 folic acid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7kdr, PDBe:7kdr, PDBj:7kdr
PDBsum7kdr
PubMed33199204
UniProtP26281|HPPK_ECOLI 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (Gene Name=folK)

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