Structure of PDB 4zdk Chain A Binding Site BS02

Receptor Information
>4zdk Chain A (length=534) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TATKHLFVSGGVASSLGKGLTASSLGQLLTARGLHVTMQKLDPYLNVDPG
TMNPFQHGEVFVTEDGAETDLDVGHYERFLDRNLPGSANVTTGQVYSTVI
AKERRGEYLGDTVQVIPHITDEIKRRILAMAQPDADGNRPDVVITEIGGT
VGDIESQPFLEAARQVRHYLGREDVFFLHVSLVPYLAPSGELKTKPTQHS
VAALRSIGITPDALILRCDRDVPEALKNKIALMCDVDIDGVISTPDAPSI
YDIPKVLHREELDAFVVRRLNLPFRDVDWTEWDDLLRRVHEPHETVRIAL
VGKYVELSDAYLSVAEALRAGGFKHRAKVEICWVASDGCETTSGAAAALG
DVHGVLIPGGFGIRGIEGKIGAIAYARARGLPVLGLCLGLQCIVIEAARS
VGLTNANSAEFDPDTPDPVIATMGGTMRLGSYPAVLEPDSVVAQAYQTTQ
VSERHRHRYEVNNAYRDKIAESGLRFSGTSPDGHLVEFVEYPPDRHPFVV
GTQAHPELKSRPTRPHPLFVAFVGAAIDYKAGEL
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
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)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain4zdk Chain A Residue 602 [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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PDB4zdk Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG.
Resolution3.49 Å
Binding residue
(original residue number in PDB)		S21 G23 K24 G25 L26 K46 E152 R223 D252 A253 I259
Binding residue
(residue number reindexed from 1)		S15 G17 K18 G19 L20 K40 E146 R217 D246 A247 I253
Annotation score3
Enzymatic activity
Enzyme Commision number 6.3.4.2: CTP synthase (glutamine hydrolyzing).
Gene Ontology
Molecular Function
GO:0003883 CTP synthase activity
GO:0004359 glutaminase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006541 glutamine metabolic process
GO:0019856 pyrimidine nucleobase biosynthetic process
GO:0044210 'de novo' CTP biosynthetic process
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4zdk, PDBe:4zdk, PDBj:4zdk
PDBsum4zdk
PubMed26097035
UniProtP9WHK7|PYRG_MYCTU CTP synthase (Gene Name=pyrG)

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