Structure of PDB 4emd Chain A Binding Site BS01

Receptor Information
>4emd Chain A (length=299) Species: 561007 (Mycobacteroides abscessus ATCC 19977) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAVTVRAPGKVNLYLAVGDLRDDGYHELTTVFHAVSLADDVTVRDADVLS
IDVVGQGEGTVPTDERNLAWQAAELFADHVGRAPDVSIFINKDIPVAGGM
AGGSADAAAVLVAMNELWHAGVPRRDLHHLAAQLGSDVPFALHGGTALGT
GRGEQLATVLARNVFHWVFAFADGGLATPQVFKEIDRLRENGDPPRLAEA
DELLGALAAGDARRLAPLLGNELQAAAVSLNPELRRTLRAGESAGALAGI
VSGSGPTCAFLCTSADDAVQVSAELAGAGVCRTVRVASGPVHGAQVIQG
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain4emd Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4emd Increasing the structural coverage of tuberculosis drug targets.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		Y36 H37 S147 R163 F193
Binding residue
(residue number reindexed from 1)		Y25 H26 S136 R152 F182
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K21 D148
Catalytic site (residue number reindexed from 1) K10 D137
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4emd, PDBe:4emd, PDBj:4emd
PDBsum4emd
PubMed25613812
UniProtB1MKD5

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