Structure of PDB 3t88 Chain D Binding Site BS01

Receptor Information
>3t88 Chain D (length=281) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEAMLYAPVEWHDCSEGFEDIRYEKSTDGIAKITINRPQVRNAFRPLTVK
EMIQALADARYDDNIGVIILTGAGDKAFCSGGDQKVRGDYGGYKDDSGVH
HLNVLDFQRQIRTCPKPVVAMVAGYSIGGGHVLHMMCDLTIAADNAIFGQ
TGPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAKQALDMGLVNTV
VPLADLEKETVRWCREMLQNSPMALRCLKAALNADCDGQAGLQELAGNAT
MLFYMTEEGQEGRNAFNQKRQPDFSKFKRNP
Ligand information
Ligand IDS0N
InChIInChI=1S/C32H45N8O20P3/c1-32(2,26(45)29(46)36-10-9-22(43)35-12-11-34-21(42)8-7-19(41)17-5-3-4-6-18(17)31(47)48)14-57-63(54,55)60-62(52,53)56-13-20-25(59-61(49,50)51)24(44)30(58-20)40-16-39-23-27(33)37-15-38-28(23)40/h3-6,15-16,20,24-26,30,44-45H,7-14H2,1-2H3,(H,34,42)(H,35,43)(H,36,46)(H,47,48)(H,52,53)(H,54,55)(H2,33,37,38)(H2,49,50,51)/t20-,24-,25-,26+,30-/m1/s1
InChIKeyQCTNXUGGWNSKFY-HSJNEKGZSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(O)=O
OpenEye OEToolkits 1.7.2CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(=O)O)O
OpenEye OEToolkits 1.7.2CC(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)[C@H](C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(=O)O)O
CACTVS 3.370CC(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)[C@@H](O)C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(O)=O
ACDLabs 12.01O=C(O)c1ccccc1C(=O)CCC(=O)NCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4OP(=O)(O)O
FormulaC32 H45 N8 O20 P3
Nameo-succinylbenzoyl-N-coenzyme A
ChEMBL
DrugBank
ZINCZINC000198511424
PDB chain3t88 Chain C Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3t88 Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member.
Resolution1.998 Å
Binding residue
(original residue number in PDB)		Y258 F270 K273
Binding residue
(residue number reindexed from 1)		Y254 F266 K269
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) G86 R91 Y97 H105 L109 G133 V136 G156 S161 D163 G164 A250 Y258
Catalytic site (residue number reindexed from 1) G82 R87 Y93 H101 L105 G129 V132 G152 S157 D159 G160 A246 Y254
Enzyme Commision number 4.1.3.36: 1,4-dihydroxy-2-naphthoyl-CoA synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0008935 1,4-dihydroxy-2-naphthoyl-CoA synthase activity
GO:0016829 lyase activity
GO:0071890 bicarbonate binding
Biological Process
GO:0009234 menaquinone biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3t88, PDBe:3t88, PDBj:3t88
PDBsum3t88
PubMed21830810
UniProtP0ABU0|MENB_ECOLI 1,4-dihydroxy-2-naphthoyl-CoA synthase (Gene Name=menB)

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