Structure of PDB 7md2 Chain D Binding Site BS01

Receptor Information
>7md2 Chain D (length=469) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PITGKVTAVIGAIVDVHFEQSELPAILNALEIKTPQGKLVLEVAQHLGEN
TVRTIAMDGTEGLVRGEKVLDTGGPISVPVGRETLGRIINVIGEPIDERG
PIKSKLRKPIHADPPSFAEQSTSAEILETGIKVVDLLAPYARGGKIGLFG
GAGVGKTVFIQELINNIAKAHGGFSVFTGVGERTREGNDLYREMKETGVI
NLEGESKVALVFGQMNEPPGARARVALTGLTIAEYFRDEEGQDVLLFIDN
IFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGLLQERITTTKKGSVTSV
QAVYVPADDLTDPAPATTFAHLDATTVLSRGISELGIYPAVDPLDSKSRL
LDAAVVGQEHYDVASKVQETLQTYKSLQDIIAILGMDELSEQDKLTVERA
RKIQRFLSQPFAVAEVFTGIPGKLVRLKDTVASFKAVLEGKYDNIPEHAF
YMVGGIEDVVAKAEKLAAE
Ligand information
Ligand IDZHD
InChIInChI=1S/C59H96O22/c1-29-20-30(2)24-40(60)43(72-15)27-42(77-55(67)34(6)25-39(71-14)23-31(3)22-33(5)50(32(4)21-29)79-56-49(64)48(63)47(62)36(8)76-56)35(7)59(69)54(73-16)53(66)58(12,44(80-59)18-17-19-70-13)81-45-26-41(61)51(37(9)74-45)78-46-28-57(11,68)52(65)38(10)75-46/h20-25,33,35-38,40-54,56,60-66,68-69H,17-19,26-28H2,1-16H3/b29-20+,30-24+,31-22+,32-21+,34-25+,39-23-/t33-,35-,36+,37-,38-,40-,41+,42+,43+,44-,45+,46+,47+,48-,49+,50-,51-,52-,53-,54-,56+,57-,58-,59+/m1/s1
InChIKeyQVIWDCUKIZPUBD-RSDTUZBPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1C=C(C=C(C=C(C(=O)OC(CC(C(C=C(C=C(C=C(C1OC2C(C(C(C(O2)C)O)O)O)C)C)C)O)OC)C(C)C3(C(C(C(C(O3)CCCOC)(C)OC4CC(C(C(O4)C)OC5CC(C(C(O5)C)O)(C)O)O)O)OC)O)C)OC)C
OpenEye OEToolkits 2.0.7C[C@@H]1/C=C(/C=C(/C=C(/C(=O)O[C@@H](C[C@@H]([C@@H](/C=C(/C=C(/C=C(/[C@H]1O[C@H]2[C@H]([C@@H]([C@H]([C@@H](O2)C)O)O)O)\C)\C)\C)O)OC)[C@@H](C)[C@]3([C@@H]([C@H]([C@]([C@H](O3)CCCOC)(C)O[C@H]4C[C@@H]([C@@H]([C@H](O4)C)O[C@H]5C[C@@]([C@@H]([C@H](O5)C)O)(C)O)O)O)OC)O)\C)\OC)\C
CACTVS 3.385COCCC[C@H]1O[C@@](O)([C@H](C)[C@@H]2C[C@H](OC)[C@H](O)/C=C(C)/C=C(C)/C=C(\C)[C@@H](O[C@@H]3O[C@@H](C)[C@H](O)[C@@H](O)[C@@H]3O)[C@H](C)\C=C(C)\C=C(OC)\C=C(/C)C(=O)O2)[C@H](OC)[C@@H](O)[C@]1(C)O[C@H]4C[C@H](O)[C@H](O[C@H]5C[C@@](C)(O)[C@H](O)[C@@H](C)O5)[C@@H](C)O4
CACTVS 3.385COCCC[CH]1O[C](O)([CH](C)[CH]2C[CH](OC)[CH](O)C=C(C)C=C(C)C=C(C)[CH](O[CH]3O[CH](C)[CH](O)[CH](O)[CH]3O)[CH](C)C=C(C)C=C(OC)C=C(C)C(=O)O2)[CH](OC)[CH](O)[C]1(C)O[CH]4C[CH](O)[CH](O[CH]5C[C](C)(O)[CH](O)[CH](C)O5)[CH](C)O4
ACDLabs 12.01CC1(O)CC(OC(C)C1O)OC1C(O)CC(OC1C)OC1(C)C(CCCOC)OC(O)(C(C)C2CC(OC)C(O)C=C(C)C=C(C)C=C(C)C(OC3OC(C)C(O)C(O)C3O)C(C)C=C(C)C=C(OC)C=C(C)C(=O)O2)C(OC)C1O
FormulaC59 H96 O22
Name(3~{E},5~{Z},7~{E},9~{R},10~{S},11~{E},13~{E},15~{E},17~{R},18~{S},20~{S})-20-[(1~{R})-1-[(2~{S},3~{R},4~{R},5~{S},6~{R})-5-[(2~{S},4~{S},5~{S},6~{R})-5-[(2~{S},4~{R},5~{R},6~{R})-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-methyl-4-oxidanyl-oxan-2-yl]oxy-3-methoxy-6-(3-methoxypropyl)-5-methyl-2,4-bis(oxidanyl)oxan-2-yl]ethyl]-5,18-dimethoxy-3,7,9,11,13,15-hexamethyl-10-[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13,15-hexaen-2-one;
Ammocidin A
ChEMBL
DrugBank
ZINC
PDB chain7md2 Chain G Residue 301 [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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PDB7md2 A Family of Glycosylated Macrolides Selectively Target Energetic Vulnerabilities in Leukemia
Resolution3.1 Å
Binding residue
(original residue number in PDB)		I390 L396 S397 D400
Binding residue
(residue number reindexed from 1)		I383 L389 S390 D393
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sun Dec 1 08:08:27 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 = '7md2', asym_id = 'D', bs = 'BS01', title = 'A Family of Glycosylated Macrolides Selectively Target Energetic Vulnerabilities in Leukemia'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7md2', asym_id='D', bs='BS01', title='A Family of Glycosylated Macrolides Selectively Target Energetic Vulnerabilities in Leukemia')
   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 = '0005524,0015986,0016887,0045261,0046034,0046933,1902600', uniprot = '', pdbid = '7md2', asym_id = 'D'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005524,0015986,0016887,0045261,0046034,0046933,1902600', uniprot='', pdbid='7md2', asym_id='D')
    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>