Structure of PDB 6eec Chain C Binding Site BS02

Receptor Information
>6eec Chain C (length=1111) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGD
VNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTY
AAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQL
VRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRK
RRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYR
KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPIT
SSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLR
TVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE
FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSH
YGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIV
YLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYM
DVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTG
MELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSN
HGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGH
NYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDE
VLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKA
REVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKI
SDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIG
QILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDG
AQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMY
IMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAY
GAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQ
SLCLNVEVLSS
Ligand information
Ligand IDC0L
InChIInChI=1S/C30H41NO7/c1-7-8-9-12-21(3)24(32)17-15-20(2)14-16-23(5)28(34)27-25(33)19-26(38-29(27)35)22(4)13-10-11-18-31-30(36)37-6/h7-8,11-12,14,16,18-19,22,24,32,34H,9-10,13,15,17H2,1-6H3,(H,31,36)/b8-7+,18-11+,20-14+,21-12+,23-16+,28-27?/t22-,24-/m1/s1
InChIKeyYSXWOFMOJMYBIO-GCBVVPFWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COC(=O)N\C=C\CC[C@@H](C)C1=CC(=O)/C(C(=O)O1)=C(O)/C(C)=C/C=C(C)/CC[C@@H](O)C(/C)=C/C/C=C/C
OpenEye OEToolkits 2.0.6CC=CCC=C(C)C(CCC(=CC=C(C)C(=C1C(=O)C=C(OC1=O)C(C)CCC=CNC(=O)OC)O)C)O
OpenEye OEToolkits 2.0.6C/C=C/C/C=C(\C)/[C@@H](CC/C(=C/C=C(\C)/C(=C1C(=O)C=C(OC1=O)[C@H](C)CC/C=C/NC(=O)OC)O)/C)O
ACDLabs 12.01CC=[C@H]C\C=C(/C)C(O)CCC(=[C@H]\C=C(/C)\C(O)=C1\C(=O)C=C(OC1=O)C(CC[C@H]=CNC(=O)OC)C)C
CACTVS 3.385COC(=O)NC=CCC[CH](C)C1=CC(=O)C(C(=O)O1)=C(O)C(C)=CC=C(C)CC[CH](O)C(C)=CCC=CC
FormulaC30 H41 N O7
Namemethyl [(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-d ihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate;
Corallopyronin A
ChEMBL
DrugBank
ZINC
PDB chain6eec 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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PDB6eec Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.
Resolution3.55 Å
Binding residue
(original residue number in PDB)		C1073 W1074 Q1077 S1120 F1121 L1124
Binding residue
(residue number reindexed from 1)		C1044 W1045 Q1048 S1091 F1092 L1095
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
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6eec, PDBe:6eec, PDBj:6eec
PDBsum6eec
PubMed30626968
UniProtP9WGY9|RPOB_MYCTU DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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