Structure of PDB 6dcf Chain C Binding Site BS01

Receptor Information
>6dcf Chain C (length=858) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQAAIDRGEEN
PVGGLEEVLAELSPIEDFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAA
PLFVTAIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRFGNRRLRTV
GELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFF
GTSQLSQFMDQNNPLSGLTHKRRLLALGVHPSHYGRMCPIETPEGPNIGL
IGSLSVYARVNPFGFIETPYRKVVTDQIDYLTADEEDRHVMDVSPRQMVS
VATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDA
GDVVVADKTGVIEEVSADYITVMADDGTRQSYRLRKFARSNHGTCANQRP
IVDAGQRVEAGQVIADGPCTQNGEMALGKNLLVAIMPWEGHNYEDAIILS
NRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERG
IVRIGAEVRDGDILVGKVTPKGETTPEERLLRAIFGEKAREVRDTSLKVP
HGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG
NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVA
KAGWNIDVAAGVPDWASKLPEELYSAPADSTVATPVFDGAQEGELAGLLG
STLPNRDGEVMVDADGKSTLFDGRSGEPFPYPVTVGYMYILKLHHLVDDK
IHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLT
IKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSS
DGAAIEMR
Ligand information
Ligand IDKNG
InChIInChI=1S/C50H67NO19/c1-21-13-12-14-29(26(6)67-48(62)49(9,10)19-34(54)55)40(57)23(3)39(56)24(4)43(68-28(8)52)22(2)32(69-35-18-33-45(27(7)66-35)64-20-63-33)15-16-65-50(11)46(60)38-36-31(53)17-30(51-47(21)61)42(59)37(36)41(58)25(5)44(38)70-50/h13,15-17,22-24,26-27,29,32-33,35,39-40,43,45,53,56-59H,12,14,18-20H2,1-11H3,(H,51,61)(H,54,55)/b16-15+,21-13-/t22-,23+,24-,26+,27-,29-,32+,33+,35+,39-,40-,43-,45-,50+/m1/s1
InChIKeyRKRZBNCHQZDJPK-UAXKWEMASA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H]1O[C@H](C[C@@H]2OCO[C@H]12)O[C@H]3\C=C\O[C@@]4(C)Oc5c(C)c(O)c6c(O)c(NC(=O)\C(=C/CC[C@H]([C@H](C)OC(=O)C(C)(C)CC(O)=O)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]3C)C)cc(O)c6c5C4=O
OpenEye OEToolkits 1.7.6Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([C@H]([C@H]([C@H]([C@@H]([C@@H]([C@H](/C=C/O[C@@]4(C(=O)c3c1O4)C)O[C@H]5C[C@H]6[C@@H]([C@H](O5)C)OCO6)C)OC(=O)C)C)O)C)O)[C@H](C)OC(=O)C(C)(C)CC(=O)O)/C)O)O
OpenEye OEToolkits 1.7.6Cc1c(c2c3c(cc(c2O)NC(=O)C(=CCCC(C(C(C(C(C(C(C(C=COC4(C(=O)c3c1O4)C)OC5CC6C(C(O5)C)OCO6)C)OC(=O)C)C)O)C)O)C(C)OC(=O)C(C)(C)CC(=O)O)C)O)O
ACDLabs 12.01c1(c3c(c(c6c2C(C(C)(OC=CC(C(C(C(C(C(C(C(CCC=C(C(=O)Nc1cc(c23)O)C)C(OC(C(C)(C)CC(=O)O)=O)C)O)C)O)C)OC(C)=O)C)OC5CC4C(OCO4)C(C)O5)O6)=O)C)O)O
CACTVS 3.385C[CH]1O[CH](C[CH]2OCO[CH]12)O[CH]3C=CO[C]4(C)Oc5c(C)c(O)c6c(O)c(NC(=O)C(=CCC[CH]([CH](C)OC(=O)C(C)(C)CC(O)=O)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]3C)C)cc(O)c6c5C4=O
FormulaC50 H67 N O19
NameKanglemycin A;
4-{(1S)-1-[(1S,2S,12S,16S,17R,18S,19R,20R,21S,22R,23S,24E)-21-(acetyloxy)-23-[(2,6-dideoxy-3,4-O-methylidene-beta-D-ribo-hexopyranosyl)oxy]-1,5,6,9,17,19-hexahydroxy-2,4,12,18,20,22-hexamethyl-11-oxo-1,2-dihydro-2,7-(epoxypentadec[1]enoimino)naphtho[2,1-b]furan-16-yl]ethoxy}-3,3-dimethyl-4-oxobutanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6dcf Chain C Residue 1201 [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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PDB6dcf Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.
Resolution3.45 Å
Binding residue
(original residue number in PDB)
G423 S425 Q426 S428 Q429 F430 D432 R445 I488 R604
Binding residue
(residue number reindexed from 1)
G201 S203 Q204 S206 Q207 F208 D210 R223 I251 R325
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0046677 response to antibiotic
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6dcf, PDBe:6dcf, PDBj:6dcf
PDBsum6dcf
PubMed30297823
UniProtP60281|RPOB_MYCS2 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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