Structure of PDB 6cce Chain C Binding Site BS02

Receptor Information
>6cce Chain C (length=1095) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQAAIDRGE
ENPVGGLEEVLAELSPIEDFSGSMSLSFSDPRFDEVKASVDECKDKDMTY
AAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQL
VRSPGVYFDETIDKSTEKTLHSVKVIPGRGAWLEFVRIDRKRRQPVTVLL
KALEQIVERFGFSEIMMGTLEKDTTSGTDEALLDIYRKLRPGEPPTKESA
QTLLENLFFKEKRYDLARVGRYKVNKKLTLTEEDVVATIEYLVRLHEGQT
SMTVPGGVEVPVEVDDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRER
MTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKR
RLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVY
ARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPTDENGR
FTEDRVMVRKKGGEVEFVSADQVDYMDVSPRQMVSVATAMIPFLEHDDAN
RALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKTGVIEEV
SADYITVMADDGTRQSYRLRKFARSNHGTCANQRPIVDAGQRVEAGQVIA
DGPCTQNGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIE
EHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILV
GKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVF
SREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVED
MPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKAGWNIDVAAGVP
DWASKLPEELYSAPADSTVATPVFDGAQEGELAGLLGSTLPNRDGEVMVD
ADGKSTLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMIT
QQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVY
EAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIEMR
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 chain6cce 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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PDB6cce Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.
Resolution3.05 Å
Binding residue
(original residue number in PDB)
R164 T424 S425 Q426 S428 Q429 F430 D432 R445 S447 L449 R456 I488 R604
Binding residue
(residue number reindexed from 1)
R144 T380 S381 Q382 S384 Q385 F386 D388 R401 S403 L405 R412 I444 R560
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

View graph for
Cellular Component
External links
PDB RCSB:6cce, PDBe:6cce, PDBj:6cce
PDBsum6cce
PubMed30297823
UniProtP60281|RPOB_MYCS2 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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