Structure of PDB 6ee1 Chain D Binding Site BS01

Receptor Information
>6ee1 Chain D (length=730) Species: 83331 (Mycobacterium tuberculosis CDC1551) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HTPFEQDFEKDVAATQRYFDSSRFAGIIRLYTARQVVEQRGTIPVDHIVA
REAAGAFYERLRELFAARKSITTFGPYSPGQAVSMKRMGIEAIYLGGWAT
SAKGSSTEDPGPDLASYPLSQVPDDAAVLVRALLTADRNQHYLRLQMSER
QRAATPAYDFRPFIIADADTGHGGDPHVRNLIRRFVEVGVPGYHIEDQRP
GTKKCGGGKVLVPSDEQIKRLNAARFQLDIMRVPGIIVARTDAEAANLID
SRADERDQPFLLGATKLDVPSYKSCFLAMVRRFYELGVKELNGHLLYALG
DSEYAAAGGWLERQGIFGLVSDAVNAWREDQQSIDGIFDQVESRFVAAWE
DDAGLMTYGEAVADVLEFAPEEWRAFAARASLHAARAKAKELGADPPWDC
ELAKTPEGYYQIRGGIPYAIAKSLAAAPFADILWMETKTADLADARQFAE
AIHAEFPDQMLAYNLSPSFNWDTTGMTDEEMRRFPEELGKMGFVFNFITY
GGHQIDGVAAEEFATALRQDGMLALARLQRKMRLVESPYRTPQTLVGGPR
SDAALAASSGRTATTVQTEVPRKLLEEWLAMWSGHYQLKDKLRVQLRPQR
AGSEVLELGIHGESDDKLANVIFQPIQDRRGRTILLVRDQNTFGAELRQK
RLMTLIHLWLVHRFKAQAVHYVTPTDDNLYQTSKMKSHGIFTEVNQEVGE
IIVAEVNHPRIAELLTPDRVALRKLITKEA
Ligand information
Ligand IDACO
InChIInChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
InChIKeyZSLZBFCDCINBPY-ZSJPKINUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
CACTVS 3.341CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)C
CACTVS 3.341CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
FormulaC23 H38 N7 O17 P3 S
NameACETYL COENZYME *A
ChEMBLCHEMBL1230809
DrugBank
ZINCZINC000008551095
PDB chain6ee1 Chain D Residue 801 [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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PDB6ee1 Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		D675 Q676 N677 T678 R684 Q685 R687 M689 T690 T711 D713 N714 Y716 Q717 K720 H724 K764
Binding residue
(residue number reindexed from 1)		D639 Q640 N641 T642 R648 Q649 R651 M653 T654 T675 D677 N678 Y680 Q681 K684 H688 K728
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y104 D123 D177 D179 H204 E206 C215 R252 E459 Q482 S489 S491
Catalytic site (residue number reindexed from 1) Y94 D113 D167 D169 H194 E196 C205 R240 E436 Q459 S466 S468
Enzyme Commision number 4.1.3.1: isocitrate lyase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004451 isocitrate lyase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle
GO:0019752 carboxylic acid metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ee1, PDBe:6ee1, PDBj:6ee1
PDBsum6ee1
PubMed31604954
UniProtQ8VJU4|ACEA2_MYCTO Isocitrate lyase 2 (Gene Name=icl2)

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