Structure of PDB 5hv1 Chain A Binding Site BS02

Receptor Information
>5hv1 Chain A (length=847) Species: 1639 (Listeria monocytogenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKPYVLKFQEIRPHSEALVGGKGMNLGACSNIEGVHVPAGFCLTTEAYKR
TLAENNEFTQLLQRLSSLKTSDMDAIREISETIRTLIQHTQIPSEIASYM
DATLLDVGGYEMPFAVRSSATAEDLPHASFAGQHDTYLNIIGKDALLQHI
SMCWASLFTERAIIYRIQNQFDHRKVQLAVVIQQMISPEASGILFTADPI
TSNRKSLSIDASFGLGEALVSGLVSADSYTVRENTITNKIIATKKLAIYS
LKEGGTETRILEKSQQTKQTLTDQQIIQLAKLGRKIEAYFGKPQDIEWCL
AEGAFYIVQSRPITTLYPIPEVNEPGNRVYISVAHQQMMTDAMKPLGLSF
YLMTTPATMYTAGGRLFVDITQSLSAKVSRDMMVNSLGQSDPLIKDALLT
VINKKGFLPSIPDSSSVFELVRNSENSIKHLKQSIETKSGSDLFDFIVED
LEELKRVLFNPTSIDAIMAGMDASAWLNEHIYQWLGEKNVADKLSESAPN
NITSQMGLELLDVADVIRPYPAVRAYLEQTKNPDFMNELATLEGGAETKK
ALEDYLQKYGMRCAGEIDLTKTRWIENPLTLIPLILSNIKNFDSSASMHK
FAQGEKEAFHKEQEILRRLQELPDGEQKAMETKEKIDILRHFIGYREYPK
YGMINRYFIYKLALLRAGEQLVKDGILQEHEDIYFLYFEELREVVRTGQV
DYELINARKRDFATFEKLTPPRILTSDGEMINGEYKRENLPKDAILGLPV
SSGTVEGRARVILEMEKADLEDGDILVTAYTDPSWTPAFVSIKGLVTEVG
GLMTHGAVIAREYGLPAVVGVENATTIIKDGQQIRINGTEGYIEILD
Ligand information
Ligand IDRFP
InChIInChI=1S/C43H58N4O12/c1-21-12-11-13-22(2)42(55)45-33-28(20-44-47-17-15-46(9)16-18-47)37(52)30-31(38(33)53)36(51)26(6)40-32(30)41(54)43(8,59-40)57-19-14-29(56-10)23(3)39(58-27(7)48)25(5)35(50)24(4)34(21)49/h11-14,19-21,23-25,29,34-35,39,49-53H,15-18H2,1-10H3,(H,45,55)/b12-11+,19-14+,22-13-,44-20+/t21-,23+,24+,25+,29-,34-,35+,39+,43-/m0/s1
InChIKeyJQXXHWHPUNPDRT-WLSIYKJHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=C\C=C(/C(=O)Nc(c2O)c(c3O)\C=N\N5CCN(CC5)C)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
ACDLabs 10.04O=C4c5c2c(O)c(\C=N\N1CCN(C)CC1)c3c(O)c2c(O)c(c5OC4(OC=CC(OC)C(C(OC(=O)C)C(C)C(O)C(C)C(O)C(C=CC=C(C(=O)N3)C)C)C)C)C
CACTVS 3.341CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C)c(C=NN5CCN(C)CC5)c(O)c4c3C2=O
CACTVS 3.341CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)\C(=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C)c(\C=N\N5CCN(C)CC5)c(O)c4c3C2=O
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)Nc(c2O)c(c3O)C=NN5CCN(CC5)C)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
FormulaC43 H58 N4 O12
NameRIFAMPICIN
ChEMBLCHEMBL374478
DrugBankDB01045
ZINCZINC000169621223
PDB chain5hv1 Chain A Residue 902 [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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PDB5hv1 Structural basis of rifampin inactivation by rifampin phosphotransferase
Resolution3.103 Å
Binding residue
(original residue number in PDB)		Y351 T355 P356 V368 F479 I487
Binding residue
(residue number reindexed from 1)		Y351 T355 P356 V368 F459 I467
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.10,Kd=79.4uM
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Nov 16 18:58:01 2024

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()
   1435     title=pdb2title(pdbid)
   1436     if bs.startswith("BS"):
=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)
   1438     else:
   1439         if lig3:
pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '5hv1', asym_id = 'A', bs = 'BS02', title = 'Structural basis of rifampin inactivation by rifampin phosphotransferase'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5hv1', asym_id='A', bs='BS02', title='Structural basis of rifampin inactivation by rifampin phosphotransferase')
   1295         display_ec(ec,csaOrig,csaRenu)
   1296     if go:
=> 1297         display_go(go,uniprot,pdbid,asym_id)
   1298     return pubmed,uniprot
   1299 
global display_go = <function display_go>, go = '0005524,0016301,0016310,0016772', uniprot = '', pdbid = '5hv1', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005524,0016301,0016310,0016772', uniprot='', pdbid='5hv1', asym_id='A')
    480         '''.replace("$namespace_link",namespace_link
    481           ).replace("$namespace",namespace
=>  482           ).replace("$uniprot",u
    483         ))
    484         for l,(term,name) in enumerate(go2aspect[Aspect]):
u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>