Structure of PDB 6hk1 Chain D Binding Site BS01

Receptor Information
>6hk1 Chain D (length=261) Species: 2186 (Methanothermococcus thermolithotrophicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDYKLKADEYNVTKAILSSAFKMWMDVIEVDVAIVGGGPSGLTAGKYLAK
EGLKVVILERHLSFGGGTWGGGMGFPYIVVEEPADEILRDAGIKLEKVED
VEGYYIADSVEVPAKLGASAIDAGAKILTSVAVEDLILREDKVAGVVVQG
YAIEKAGLHVDPITINAKYVIDATGHDASVTTTLARKNKDLGIEVPGEKS
MWADKGENSLLRNTREVYPGLFVCGMAANAVHAGYRMGAIFGGMYLSGKK
CAEMILEKLNK
Ligand information
Ligand ID48F
InChIInChI=1S/C15H23N5O14P2/c16-13-9-14(18-4-17-13)20(5-19-9)15-12(26)11(25)8(33-15)3-32-36(29,30)34-35(27,28)31-2-7(23)10(24)6(22)1-21/h4-5,7-8,10-12,15,21,23-26H,1-3H2,(H,27,28)(H,29,30)(H2,16,17,18)/t7-,8-,10+,11-,12-,15-/m1/s1
InChIKeyHMVGRTYSZXZGQZ-GHVQHMAVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(C(=O)CO)O)O)O)O)N
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)[CH](O)C(=O)CO)[CH](O)[CH]3O
ACDLabs 12.01O=C(CO)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)[C@@H](O)C(=O)CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.9.2c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@H]([C@H](C(=O)CO)O)O)O)O)N
FormulaC15 H23 N5 O14 P2
Name[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R)-2,3,5-tris(oxidanyl)-4-oxidanylidene-pentyl] hydrogen phosphate
ChEMBL
DrugBank
ZINCZINC000584904643
PDB chain6hk1 Chain D Residue 308 [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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PDB6hk1 Protein crystal structure determination with the crystallophore, a nucleating and phasing agent.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		V35 G36 G38 P39 S40 L58 E59 R60 H61 G66 V133 T174 G175 S179 G225 M226 G238 F241 M244
Binding residue
(residue number reindexed from 1)		V35 G36 G38 P39 S40 L58 E59 R60 H61 G66 V133 T174 G175 S179 G225 M226 G238 F241 M244
Annotation score2
Enzymatic activity
Enzyme Commision number 2.4.2.59: sulfide-dependent adenosine diphosphate thiazole synthase.
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0016740 transferase activity
GO:0016763 pentosyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0009228 thiamine biosynthetic process
GO:0009229 thiamine diphosphate biosynthetic process
GO:0052837 thiazole biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6hk1, PDBe:6hk1, PDBj:6hk1
PDBsum6hk1
PubMed31396026
UniProtA0A5H1ZR31

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