Structure of PDB 6m7j Chain D Binding Site BS04

Receptor Information
>6m7j Chain D (length=1266) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAMLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFC
EKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELA
APVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNEL
STLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVR
DGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRY
GEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKV
VAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVI
NRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRP
LKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMA
LELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLL
NRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLS
AEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGE
YQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEA
ELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIIN
DLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDH
YEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNP
IITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLE
YFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIV
VELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPE
IDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIV
AAQSIGEPGTQLTMTGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGER
FYKITIVPDDGGEEVVYDKISKRQRLRVFKRVLSDGDHVEVGQQLMEGSA
DPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVT
IIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLA
TDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINR
YRNIAVQPTEEARAAA
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 chain6m7j Chain D Residue 1404 [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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PDB6m7j Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.
Resolution4.4 Å
Binding residue
(original residue number in PDB)
K407 K420 L1221 K1249 V1252
Binding residue
(residue number reindexed from 1)
K409 K422 L1205 K1233 V1236
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6m7j, PDBe:6m7j, PDBj:6m7j
PDBsum6m7j
PubMed30626968
UniProtP9WGY7|RPOC_MYCTU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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