Rv0667

Tuberculist information
Gene namerpoB
Protein functionDNA-directed RNA polymerase (beta chain) RpoB (transcriptase beta chain) (RNA polymerase beta subunit)
Functional category(tuberculist)information pathways
Gene location(kb)759.807
Molecular mass(da)129218
External sites TB Database TubercuList WebTB
Protein sequence
Number of amino acids : 1172
	  		  	1    LADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIG   60
			  	61   SPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKD  120
			  	121  MTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVY  180
			  	181  FDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSE  240
			  	241  QIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRY  300
			  	301  DLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVE  360
			  	361  TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA  420
			  	421  IKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI  480
			  	481  ETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANS  540
			  	541  PIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRAL  600
			  	601  MGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGT  660
			  	661  RRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPW  720
			  	721  EGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDE  780
			  	781  RGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGK  840
			  	841  VIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPF  900
			  	901  LADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEA  960
			  	961  QPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVG 1020
			  	1021 YMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQ 1080
			  	1081 ELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIE 1140
			  	1141 LREGEDEDLERAAANLGINLSRNESASVEDLA

Known structures in the PDB
PDB ID4KBJ
Total residue count818
Number of chains2
MethodX-RAY
Resolution2.45
PDB ID4KBM
Total residue count571
Number of chains2
MethodX-RAY
Resolution2.11
1 118 235 352 469 586 703 820 937 1054 1171 Range: 52 to 434  |  Coverage: 32% RNA_pol_Rpb2_1 Range: 181 to 379  |  Coverage: 16% RNA_pol_Rpb2_2 Range: 438 to 507  |  Coverage: 5% RNA_pol_Rpb2_3 Range: 516 to 582  |  Coverage: 5% RNA_pol_Rpb2_45 Range: 588 to 1062  |  Coverage: 40% RNA_pol_Rpb2_6 Range: 1064 to 1140  |  Coverage: 6% RNA_pol_Rpb2_7 Range: 33 to 112  |  Coverage: 6% 1 Range: 18 to 1171  |  Coverage: 98% 1
Number of amino acids : 1172
Domains assigned based on sequence. Mtb Structural proteome models CHOPIN models
Profile-based domain assignment
Structural/Functional domain familyPfam acc.no./SCOP IDDomain Region
RNA_pol_Rpb2_1PF0456352-434
RNA_pol_Rpb2_2PF04561181-379
RNA_pol_Rpb2_3PF04565438-507
RNA_pol_Rpb2_45PF10385516-582
RNA_pol_Rpb2_6PF00562588-1062
RNA_pol_Rpb2_7PF045601064-1140
Mtb Structural Proteome models
Model Number1
Model nameRv0667
Template1YNJ    CPDBCREDO
Template coverage4_1114
Template Identity(%)51.4
Model coverage(%)94.8
Normalized DOPE score0.537

Structure Models from Chopin
Model Number1
Profilee.29.1.1
Click for model details
zscore70.93
Residue begin18
Residue end1171
Binding pockets
STRING
Cytoscape Web will replace the contents of this div with protein-protein interaction network.
Protein interacting with Rv0667Gene nameConfidence Score
Rv0668rpoC0.999
Rv0668rpoC0.999
Rv3457crpoA0.999
Rv0682rpsL0.999
Rv3457crpoA0.999
Rv0668rpoC0.999
Rv3457crpoA0.999
Rv0668rpoC0.999
Rv0668rpoC0.999
Rv0639nusG0.998
Rv0639nusG0.998
Rv0721rpsE0.997
Rv0721rpsE0.997
Rv2710sigB0.996
Rv0683rpsG0.996
Rv2710sigB0.996
Rv2710sigB0.996
Rv2710sigB0.996
Rv0700rpsJ0.996
Rv0640rplK0.995
Rv0707rpsC0.995
Rv0707rpsC0.995
Rv0652rplL0.995
Rv0640rplK0.995
Rv0684fusA10.994
Rv0684fusA10.994
Rv0684fusA10.994
Rv0684fusA10.994
Rv0684fusA10.994
Rv2703sigA0.993
Rv0641rplA0.993
Rv2703sigA0.993
Rv2783cgpsI0.993
Rv2783cgpsI0.993
Rv2783cgpsI0.993
Rv2703sigA0.993
Rv2783cgpsI0.993
Rv2703sigA0.993
Rv2783cgpsI0.993
Rv3459crpsK0.992
Rv0702rplD0.992
Rv0704rplB0.992
Rv0704rplB0.992
Rv0701rplC0.991
Rv3460crpsM0.991
Rv0732secY0.991
Rv3458crpsD0.991
Rv3458crpsD0.991
Rv1617pykA0.99
Rv2462ctig0.99
Rv1699pyrG0.99
Rv0716rplE0.99
Rv2462ctig0.99
Rv0651rplJ0.99
Rv0716rplE0.99
Rv2462ctig0.99
Rv0685tuf0.99
Rv0708rplP0.99
Rv0685tuf0.99
Rv0719rplF0.99
Rv0685tuf0.99
Rv0714rplN0.99
Rv1617pykA0.99
Rv1699pyrG0.99
Rv0705rpsS0.989
Rv2583crelA0.987
Rv0001dnaA0.987
Rv2583crelA0.987
Rv2583crelA0.987
Rv2583crelA0.987
Rv0001dnaA0.987
Rv0718rpsH0.986
Rv0723rplO0.984
Rv3443crplM0.983
Rv0710rpsQ0.983
Rv0440groEL20.982
Rv0006gyrA0.979
Rv0006gyrA0.979
Rv3456crplQ0.977
Rv0703rplW0.977
Rv2445cndkA0.975
Rv0005gyrB0.974
Rv0005gyrB0.974
Rv0005gyrB0.974
Rv0005gyrB0.974
Rv2043cpncA0.973
Rv2678chemE0.973
Rv2150cftsZ0.972
Rv3417cgroEL10.972
Rv2150cftsZ0.972
Rv2839cinfB0.971
Rv2839cinfB0.971
Rv2839cinfB0.971
Rv2839cinfB0.971
Rv3442crpsI0.97
Rv0706rplV0.967
Rv1848ureA0.967
Rv0350dnaK0.966
Rv3846sodA0.965
Rv3846sodA0.965
Rv2428ahpC0.965
Rv2906ctrmD0.961
Rv0720rplR0.96
Rv3286csigF0.958
Rv3286csigF0.958
Rv3286csigF0.958
Rv1908ckatG0.951
Rv1080cgreA0.95
Rv1297rho0.95
Rv2889ctsf0.95
Rv1297rho0.95
Rv2889ctsf0.95
Rv1297rho0.95
Rv1080cgreA0.95
Rv0120cfusA20.949
Rv0120cfusA20.949
Rv0120cfusA20.949
Rv0733adk0.949
Rv0120cfusA20.949
Rv0120cfusA20.949
Rv0715rplX0.946
Rv1020mfd0.946
Rv1020mfd0.946
Rv1020mfd0.946
Rv1020mfd0.946
Rv2533cnusB0.945
Rv1641infC0.943
Rv2457cclpX0.943
Rv1641infC0.943
Rv2457cclpX0.943
Rv2457cclpX0.943
Rv2890crpsB0.942
Rv2441crpmA0.94
Rv2720lexA0.939
Rv2720lexA0.939
Rv2580chisS0.937
Rv2580chisS0.937
Rv0620galK0.935
Rv0620galK0.935
Rv0620galK0.935
Rv0717rpsN10.934
Rv0321dcd0.931
Rv2841cnusA0.93
Rv2841cnusA0.93
Rv2904crplS0.928
Rv2056crpsN20.923
Rv3646ctopA0.922
Rv3646ctopA0.922
Rv3646ctopA0.922
Rv1023eno0.921
Rv1023eno0.921
Rv1625ccya0.92
Rv2343cdnaG0.92
Rv2343cdnaG0.92
Rv0634BrpmG20.92
Rv2343cdnaG0.92
Rv2343cdnaG0.92
Rv2343cdnaG0.92
Rv1310atpD0.919
Rv1310atpD0.919
Rv1310atpD0.919
Rv2785crpsO0.917
Rv2883cpyrH0.916
Rv2916cffh0.914
Rv2916cffh0.914
Rv2916cffh0.914
Rv1341Rv13410.913
Rv1308atpA0.912
Rv0041leuS0.912
Rv0041leuS0.912
Rv0041leuS0.912
Rv2992cgltS0.912
Rv1308atpA0.912
Rv1308atpA0.912
Rv1689tyrS0.91
Rv1689tyrS0.91
Rv2461cclpP10.907
Rv3608cfolP10.905
Rv3133cdevR0.905
Rv3133cdevR0.905
Rv1021Rv10210.901
Rv3419cgcp0.901
Potential ligand/drug binding sites
No binding sites identified
Similarity to known drug target from sensitive sequence analysis
No drug targets
List of small molecules tested from TIBLE
  View results in TIBLE page
NameAffinityAssay descriptionDOI
CHEMBL1909658IC50 = 0.013 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1909658logIC50 = -1.8767 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911286Ratio IC50 = 2 NoneRatio of compound IC50 to Rifamycin S IC50 for wild type Mycobacterium tuberculosis RNA polymerasehttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911286IC50 = 0.021 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911286logIC50 = -1.6795 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911287logIC50 = 0.6441 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911287IC50 = 4.4 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911289logIC50 = -0.2984 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911289IC50 = 0.503 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911295logIC50 = 1.1879 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911295IC50 = 15.4 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911296IC50 = 0.015 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911296logIC50 = -1.8199 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911298IC50 = 0.142 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911298logIC50 = -0.8462 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911298Ratio IC50 = 10 NoneRatio of compound IC50 to Rifampin S IC50 for wild type Mycobacterium tuberculosis RNA polymerasehttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911306logIC50 = -0.85567 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL1911306IC50 = 0.139 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL236921logIC50 = -2.1734 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL236921IC50 < 0.01 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL374478logIC50 = -2.3986 NoneInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CHEMBL374478IC50 < 0.01 uMInhibition of wild type Mycobacterium tuberculosis RNA polymerase after 10 mins using ribo green staining by rolling circle transcription assayhttp://www.ncbi.nlm.nih.gov/pubmed/21903392
CDD-341172NoneNoneNone
CDD-990NoneNoneNone
CDD-991NoneNoneNone
Off-target activity - ligand based from TIBLE
  View results in TIBLE page
Predicted off-targetMethodSummaryFull results
Nuclear receptor subfamily 1 group I member 2 1SKXPharmMapper9 hydroph + 1 HB + 0 pos/neg + 0 aromLink
Corticosteroid 11-beta-dehydrogenase isozyme 1 3CH6PharmMapper6 hydroph + 1 HB + 0 pos/neg + 0 aromLink
Alpha-tocopherol transfer protein 1R5LPharmMapper11 hydroph + 1 HB + 0 pos/neg + 0 aromLink
Vitamin D3 receptor 1DB1PharmMapper9 hydroph + 4 HB + 0 pos/neg + 0 aromLink
RAC-alpha serine/threonine-protein kinase 1UNQPharmMapper0 hydroph + 9 HB + 3 pos/neg + 0 aromLink
DNA directed RNA polymerase  PASSPa = 0.729 & SM = CHEMBL1911296Link
Heat shock protein HSP 90-alpha SEAE_value = 6.49e-57 & MaxTC = 0.36Link
Heat shock protein HSP 90-beta SEAE_value = 3.09e-56 & MaxTC = 0.36Link
Small molecules involved in protein-protein complex from TIMBAL .Proteins similar to Mtb based on sequence analysis.
Data not available
STITCH interactions  
Chemical NameConfidence scoreMolecular Weight
rifabutinPubChem0.97847.005
rifampicinPubChem0.946822.94
rifamycinPubChem0.931697.769
KRM-1648PubChem0.905941.073
guanosine tetraphosphatePubChem0.903603.16
adenosine triphosphatePubChem0.9507.181
uridine triphosphatePubChem0.9484.141
ara-CTPPubChem0.9483.156
guanosine triphosphatePubChem0.9523.18
cytidine triphosphatePubChem0.9483.156
BAAPubChem0.888191.269
isoniazidPubChem0.864137.139
magnesiumPubChem0.83324.305
tagetitoxinPubChem0.827416.298
streptomycinPubChem0.804581.574
zincPubChem0.80365.409
rifapentinePubChem0.799877.031
AFBPubChem0.772278.343
MABAPubChem0.766137.136
alpha-l-sorbofuranosePubChem0.76180.156
clarithromycinPubChem0.749747.953
ethambutolPubChem0.749204.31
3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalosePubChem0.739340.327
rifampin and isoniazidPubChem0.739960.08
pyrazinamidePubChem0.734123.113
cyclic AMPPubChem0.723329.206
free acidPubChem0.715600.7
kanamycinPubChem0.711484.499
DB08266PubChem0.704417.495
phosphatePubChem0.70496.9872
2-methyl-2,4-pentanediolPubChem0.704118.174
Pb2+PubChem0.704207.2
(4s)-2-Methyl-2,4-PentanediolPubChem0.704118.174
hydron diphosphatePubChem0.704391.981
alpha,beta-methylene ATPPubChem0.704505.208