Structure of PDB 3udv Chain A Binding Site BS01

Receptor Information
>3udv Chain A (length=154) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQ
PDYLNAAVALETSLAPEELLNHTQRIELQQGRERWGPRTLDLDIMLFGNE
VINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDK
LNKW
Ligand information
Ligand IDJ1C
InChIInChI=1S/C26H36N12O5S/c1-26(2)18(33-15-20(36-26)34-25(28)35-22(15)41)23(42)29-5-8-37-6-3-12(4-7-37)44-9-13-16(39)17(40)24(43-13)38-11-32-14-19(27)30-10-31-21(14)38/h10-13,16-17,24,39-40H,3-9H2,1-2H3,(H,29,42)(H2,27,30,31)(H4,28,34,35,36,41)/t13-,16-,17-,24-/m1/s1
InChIKeyLXHMIPYFQUZUMS-FUKGTJLDSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC1(C)NC2=C(N=C1C(=O)NCCN3CCC(CC3)SC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)C(=O)NC(=N2)N
OpenEye OEToolkits 1.7.2CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCCN3CCC(CC3)SCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)C
OpenEye OEToolkits 1.7.2CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCCN3CCC(CC3)SC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)C
CACTVS 3.370CC1(C)NC2=C(N=C1C(=O)NCCN3CCC(CC3)SC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)C(=O)NC(=N2)N
ACDLabs 12.01O=C2NC(=NC=1NC(C(=NC=12)C(=O)NCCN6CCC(SCC5OC(n4cnc3c(ncnc34)N)C(O)C5O)CC6)(C)C)N
FormulaC26 H36 N12 O5 S
Name5'-S-[1-(2-{[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)carbonyl]amino}ethyl)piperidin-4-yl]-5'-thioadenosine
ChEMBLCHEMBL1928285
DrugBank
ZINCZINC000073198734
PDB chain3udv Chain A Residue 171 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3udv Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties.
Resolution1.88 Å
Binding residue
(original residue number in PDB)		T42 L45 Y53 N55 W89 G90 R92 D95 D97 I98 R110 L111 T112 F123
Binding residue
(residue number reindexed from 1)		T42 L45 Y53 N55 W85 G86 R88 D91 D93 I94 R106 L107 T108 F119
Annotation score1
Binding affinityMOAD: Kd=2.55uM
PDBbind-CN: -logKd/Ki=5.59,Kd=2.55uM
BindingDB: Kd=2550nM,IC50=3160nM
Enzymatic activity
Catalytic site (original residue number in PDB) R82 R92 D95 D97
Catalytic site (residue number reindexed from 1) R82 R88 D91 D93
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:3udv, PDBe:3udv, PDBj:3udv
PDBsum3udv
PubMed22169600
UniProtP26281|HPPK_ECOLI 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (Gene Name=folK)

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