Structure of PDB 4i52 Chain F Binding Site BS01

Receptor Information
>4i52 Chain F (length=274) Species: 1111708 (Synechocystis sp. PCC 6803 substr. Kazusa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DWHIAKHYDDILYYKAGGIAKIVINRPHKRNAFRPQTVFELYDAFCNARE
DNRIGVVLLTGAGPHSDGKYAFCSGGDQSVRGEGGYIDDQGTPRLNVLDL
QRLIRSMPKVVIALVAGYAIGGGHVLHLVCDLTIAADNAIFGQTGPKVGS
FDGGFGSSYLARIVGQKKAREIWYLCRQYSAQEAERMGMVNTVVPVDRLE
EEGIQWAKEILSKSPLAIRCLKAAFNADCDGQAGLQELAGNATLLYYMTE
EGSEGKQAFLEKRPPDFSQYPWLP
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 chain4i52 Chain F Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4i52 Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily
Resolution2.35 Å
Binding residue
(original residue number in PDB)		H29 K30 R31 A33 S75 G76 G77 D78 Q79 Y87 V98 Y119 I121 G123 T145 V149 S151 F152
Binding residue
(residue number reindexed from 1)		H28 K29 R30 A32 S74 G75 G76 D77 Q78 Y86 V97 Y118 I120 G122 T144 V148 S150 F151
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) G77 R82 Y87 R95 L99 G123 V126 G146 S151 D153 G154 A240 Y248
Catalytic site (residue number reindexed from 1) G76 R81 Y86 R94 L98 G122 V125 G145 S150 D152 G153 A239 Y247
Enzyme Commision number 4.1.3.36: 1,4-dihydroxy-2-naphthoyl-CoA synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008935 1,4-dihydroxy-2-naphthoyl-CoA synthase activity
GO:0016829 lyase activity
Biological Process
GO:0009234 menaquinone biosynthetic process
GO:0042372 phylloquinone 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:4i52, PDBe:4i52, PDBj:4i52
PDBsum4i52
PubMed23658663
UniProtP73495

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