Structure of PDB 4i42 Chain H Binding Site BS01

Receptor Information
>4i42 Chain H (length=284) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IYPDEAMLYAPVEWHDCSEGFEDIRYEKSTDGIAKITINRPQVRNAFRPL
TVKEMIQALADARYDDNIGVIILTGAGDKAFCSGGDQKVRGDYGGYKDDS
GVHHLNVLDFQRQIRTCPKPVVAMVAGYSIGGGHVLHMMCDLTIAADNAI
FGQTGPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAKQALDMGLV
NTVVPLADLEKETVRWCREMLQNSPMALRCLKAALNADCDGQAGLQELAG
NATMLFYMTEEGQEGRNAFNQKRQPDFSKFKRNP
Ligand information
Ligand ID1HA
InChIInChI=1S/C32H42N7O18P3S/c1-32(2,26(43)29(44)35-10-9-21(40)34-11-12-61-31(45)19-8-7-17-5-3-4-6-18(17)23(19)41)14-54-60(51,52)57-59(49,50)53-13-20-25(56-58(46,47)48)24(42)30(55-20)39-16-38-22-27(33)36-15-37-28(22)39/h3-8,15-16,20,24-26,30,41-43H,9-14H2,1-2H3,(H,34,40)(H,35,44)(H,49,50)(H,51,52)(H2,33,36,37)(H2,46,47,48)/t20-,24-,25-,26+,30-/m1/s1
InChIKeyZHSLHXZSNOSMQG-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)NCCSC(=O)c4ccc5ccccc5c4O
OpenEye OEToolkits 1.7.6CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)c4ccc5ccccc5c4O)O
OpenEye OEToolkits 1.7.6CC(C)(COP(=O)(O)OP(=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)NCCSC(=O)c4ccc5ccccc5c4O)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)NCCSC(=O)c4ccc5ccccc5c4O
ACDLabs 12.01O=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)c5ccc4ccccc4c5O
FormulaC32 H42 N7 O18 P3 S
Name1-hydroxy-2-naphthoyl-CoA
ChEMBL
DrugBank
ZINCZINC000206504123
PDB chain4i42 Chain H Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4i42 Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme A synthase from the crotonase fold superfamily
Resolution1.848 Å
Binding residue
(original residue number in PDB)		V44 R45 S84 G85 G86 D87 Q88 K89 V108 L109 Y129 G133 T155 V159 S161 F162
Binding residue
(residue number reindexed from 1)		V43 R44 S83 G84 G85 D86 Q87 K88 V107 L108 Y128 G132 T154 V158 S160 F161
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) G85 R90 Y96 H104 L108 G132 V135 G155 S160 D162 G163 A249 Y257
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:4i42, PDBe:4i42, PDBj:4i42
PDBsum4i42
PubMed23658663
UniProtP0ABU0|MENB_ECOLI 1,4-dihydroxy-2-naphthoyl-CoA synthase (Gene Name=menB)

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