Structure of PDB 4onc Chain B Binding Site BS02

Receptor Information
>4onc Chain B (length=282) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FPQLPPAPDDYPTFPDTSTWPVVFPELPAAPGPCRPPQHTSKAAAPRIPA
DRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKW
LSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSRP
RLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVAA
GRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEY
IFQDKLWPDYDRRDLWAACEEYASRTRRFGSA
Ligand information
Ligand ID40B
InChIInChI=1S/C19H18O7P2/c20-19(27(21,22)23,28(24,25)26)18-11-5-10-17(13-18)16-9-4-8-15(12-16)14-6-2-1-3-7-14/h1-13,20H,(H2,21,22,23)(H2,24,25,26)
InChIKeyQLUPVXJJKKYIHH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)c2cccc(c2)c3cccc(c3)C(O)(P(=O)(O)O)P(=O)(O)O
ACDLabs 12.01O=P(O)(O)C(O)(c1cccc(c1)c3cccc(c2ccccc2)c3)P(=O)(O)O
CACTVS 3.370OC(c1cccc(c1)c2cccc(c2)c3ccccc3)([P](O)(O)=O)[P](O)(O)=O
FormulaC19 H18 O7 P2
Name[hydroxy(1,1':3',1''-terphenyl-3-yl)methanediyl]bis(phosphonic acid)
ChEMBLCHEMBL215413
DrugBank
ZINCZINC000035049988
PDB chain4onc Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4onc Structure and Inhibition of Tuberculosinol Synthase and Decaprenyl Diphosphate Synthase from Mycobacterium tuberculosis
Resolution1.83 Å
Binding residue
(original residue number in PDB)		G77 N78 G79 R80 R89 R127
Binding residue
(residue number reindexed from 1)		G63 N64 G65 R66 R75 R113
Annotation score1
Binding affinityMOAD: Kd=410nM
Enzymatic activity
Catalytic site (original residue number in PDB) D76 H93 I187
Catalytic site (residue number reindexed from 1) D62 H79 I173
Enzyme Commision number 2.5.1.86: trans,polycis-decaprenyl diphosphate synthase.
2.5.1.87: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific].
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004659 prenyltransferase activity
GO:0008834 di-trans,poly-cis-undecaprenyl-diphosphate synthase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0030145 manganese ion binding
GO:0033850 Z-farnesyl diphosphate synthase activity
GO:0045547 dehydrodolichyl diphosphate synthase activity
GO:0046872 metal ion binding
GO:0052923 all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity
Biological Process
GO:0016094 polyprenol 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:4onc, PDBe:4onc, PDBj:4onc
PDBsum4onc
PubMed24475925
UniProtP9WFF7|DPDS_MYCTU Decaprenyl diphosphate synthase (Gene Name=uppS)

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