Structure of PDB 4dxl Chain A Binding Site BS02

Receptor Information
>4dxl Chain A (length=304) Species: 561007 (Mycobacteroides abscessus ATCC 19977) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSDWVPTGAVTVRAPGKVNLYLAVGDLRDDGYHELTTVFHAVSLADDVTV
RDADVLSIDVVGQGEGTVPTDERNLAWQAAELFADHVGRAPDVSIFINKD
IPVAGGMAGGSADAAAVLVAMNELWHAGVPRRDLHHLAAQLGSDVPFALH
GGTALGTGRGEQLATVLARNVFHWVFAFADGGLATPQVFKEIDRLRENGD
PPRLAEADELLGALAAGDARRLAPLLGNELQAAAVSLNPELRRTLRAGES
AGALAGIVSGSGPTCAFLCTSADDAVQVSAELAGAGVCRTVRVASGPVHG
AQVI
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
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)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain4dxl Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4dxl Increasing the structural coverage of tuberculosis drug targets.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N78 L79 K103 V107 A108 G110 A112 G113 G114 D117 D148 T189
Binding residue
(residue number reindexed from 1)		N74 L75 K99 V103 A104 G106 A108 G109 G110 D113 D144 T185
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K21 D148
Catalytic site (residue number reindexed from 1) K17 D144
Enzyme Commision number 2.7.1.148: 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0050515 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0016310 phosphorylation
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4dxl, PDBe:4dxl, PDBj:4dxl
PDBsum4dxl
PubMed25613812
UniProtB1MKD5

[Back to BioLiP]