SInCRe - Rv3133c

Tuberculist information

Gene name	devR
Protein function	Two component transcriptional regulatory protein DevR (probably LuxR/UhpA-family)
Functional category(tuberculist)	regulatory proteins
Gene location(kb)	3499.26
Molecular mass(da)	23261.9
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 217

	  		  	1    VVKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDG   60
			  	61   NGIELCRDLLSRMPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDVGA  120
			  	121  GRSLLDNRAAAALMAKLRGAAEKQDPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKT  180
			  	181  VKNYVSRLLAKLGMERRTQAAVFATELKRSRPPGDGP

Known structures in the PDB

	PDB ID	1ZLJ
	Total residue count	624
	Number of chains	8
	Method	X-RAY
	Resolution	2

	PDB ID	1ZLK
	Total residue count	276
	Number of chains	4
	Method	X-RAY
	Resolution	3.1

	PDB ID	3C3W
	Total residue count	450
	Number of chains	2
	Method	X-RAY
	Resolution	2.2

	PDB ID	3C57
	Total residue count	190
	Number of chains	2
	Method	X-RAY
	Resolution	1.7

Number of amino acids : 217

Domains assigned based on sequence.

Mtb Structural proteome models

CHOPIN models

Profile-based domain assignment

Structural/Functional domain family	Pfam acc.no./SCOP ID	Domain Region
Response_reg	PF00072	4-116
GerE	PF00196	147-204

Mtb Structural Proteome models

Model Number	1
Model name	Rv3133c_1zlj_A
Template	1ZLJ APDB CREDO
Template coverage	145_213
Template Identity(%)	100.0
Model coverage(%)	31.3
Normalized DOPE score	-2.361

Model Number	2
Model name	Rv3133c_3c57_A
Template	3C57 APDB CREDO
Template coverage	149_199
Template Identity(%)	100.0
Model coverage(%)	23.0
Normalized DOPE score	-2.278

Model Number	3
Model name	Rv3133c
Template	1ZLJ BPDB CREDO
Template coverage	141_209
Template Identity(%)	95.7
Model coverage(%)	31.3
Normalized DOPE score	-2.168

Model Number	4
Model name	Rv3133c_1zlk_A
Template	1ZLK APDB CREDO
Template coverage	145_209
Template Identity(%)	100.0
Model coverage(%)	29.5
Normalized DOPE score	-1.952

Model Number	5
Model name	Rv3133c_3c3w_A
Template	3C3W APDB CREDO
Template coverage	1_211
Template Identity(%)	100.0
Model coverage(%)	96.8
Normalized DOPE score	-1.607

Model Number	6
Model name	Rv3133c.1
Template	2GWR APDB CREDO
Template coverage	7_228
Template Identity(%)	22.6
Model coverage(%)	97.2
Normalized DOPE score	-0.119

Structure Models from Chopin

Model Number	1
Profile	a.4.6.2, c.23.1.1 - 1.10.10.10, 3.40.50.2300 Click for model details
zscore	31.48
Residue begin	1
Residue end	210

Model Number	2
Profile	a.4.6.2 - 1.10.10.10 Click for model details
zscore	19
Residue begin	145
Residue end	213

Model Number	3
Profile	c.23.1.1 - 3.40.50.2300 Click for model details
zscore	11.52
Residue begin	1
Residue end	216

Binding pockets

STRING

Cytoscape Web will replace the contents of this div with protein-protein interaction network.

Protein interacting with Rv3133c	Gene name	Confidence Score
Rv3132c	devS	0.999
Rv3132c	devS	0.999
Rv3132c	devS	0.999
Rv3134c	Rv3134c	0.993
Rv2031c	hspX	0.968
Rv2027c	dosT	0.963
Rv2027c	dosT	0.963
Rv2027c	dosT	0.963
Rv2027c	dosT	0.963
Rv0667	rpoB	0.905
Rv0667	rpoB	0.905
Rv0667	rpoB	0.905
Rv0667	rpoB	0.905
Rv0667	rpoB	0.905
Rv0667	rpoB	0.905

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv3133c.1	3	2y7j_B49_D_1294 PDB CREDO	0.649	0.125	0.649	0.001
Rv3133c.1	3	2y7j_B49_A_1294 PDB CREDO	0.630	0.145	0.602	0.002
Rv3133c.1	3	1cqp_803_A_311 PDB CREDO	0.618	0.158	0.591	0.002
Rv3133c.1	3	1pcg_EST_B_2 PDB CREDO	0.617	0.159	0.590	0.003
Rv3133c.1	3	1qku_EST_A_600 PDB CREDO	0.612	0.165	0.585	0.003
Rv3133c.1	3	1qku_EST_B_600 PDB CREDO	0.612	0.165	0.585	0.003
Rv3133c.1	3	1qku_EST_C_600 PDB CREDO	0.611	0.166	0.584	0.003
Rv3133c.1	3	1ere_EST_E_600 PDB CREDO	0.610	0.167	0.583	0.003
Rv3133c.1	3	1gwr_EST_B_600 PDB CREDO	0.609	0.169	0.582	0.003
Rv3133c.1	3	1ere_EST_A_600 PDB CREDO	0.608	0.170	0.581	0.003
Rv3133c.1	3	1pg2_ADN_A_552 PDB CREDO	0.637	0.138	0.581	0.003
Rv3133c.1	3	1ere_EST_B_600 PDB CREDO	0.607	0.171	0.580	0.003
Rv3133c.1	3	1g50_EST_B_1600 PDB CREDO	0.607	0.171	0.580	0.003
Rv3133c.1	3	1gwr_EST_A_600 PDB CREDO	0.606	0.172	0.579	0.003
Rv3133c.1	3	1cqp_803_B_311 PDB CREDO	0.599	0.180	0.573	0.003
Rv3133c.1	1	1hwk_117_B_1 PDB CREDO	0.587	0.194	0.571	0.004
Rv3133c.1	3	2fum_MIX_B_1539 PDB CREDO	0.704	0.078	0.569	0.004
Rv3133c.1	3	1dtl_BEP_A_204 PDB CREDO	0.696	0.084	0.562	0.004
Rv3133c.1	3	2j7x_EST_A_1454 PDB CREDO	0.614	0.162	0.562	0.004
Rv3133c.1	3	3hm1_J3Z_A_2 PDB CREDO	0.588	0.194	0.562	0.004
Rv3133c.1	3	1a52_EST_A_1 PDB CREDO	0.613	0.164	0.562	0.004
Rv3133c.1	3	1a52_EST_B_2 PDB CREDO	0.613	0.164	0.562	0.004
Rv3133c.1	3	1qkt_EST_A_600 PDB CREDO	0.613	0.164	0.562	0.004
Rv3133c.1	3	2ocf_EST_A_596 PDB CREDO	0.613	0.164	0.562	0.004
Rv3133c.1	3	1pcg_EST_A_1 PDB CREDO	0.611	0.166	0.560	0.004
Rv3133c.1	1	1hwk_117_A_2 PDB CREDO	0.576	0.210	0.559	0.004
Rv3133c.1	1	1hwk_117_C_4 PDB CREDO	0.575	0.210	0.558	0.004
Rv3133c.1	3	1ere_EST_F_600 PDB CREDO	0.609	0.168	0.558	0.004
Rv3133c.1	3	3hm1_J3Z_B_1 PDB CREDO	0.609	0.168	0.558	0.004
Rv3133c.1	3	2zva_1N1_A_513 PDB CREDO	0.718	0.068	0.558	0.004
Rv3133c.1	1	3gcs_BAX_A_401 PDB CREDO	0.574	0.211	0.558	0.004
Rv3133c.1	3	1g50_EST_C_2600 PDB CREDO	0.608	0.169	0.557	0.004
Rv3133c.1	3	1ere_EST_C_600 PDB CREDO	0.606	0.172	0.555	0.005
Rv3133c.1	3	3oll_EST_A_600 PDB CREDO	0.606	0.172	0.555	0.005
Rv3133c.1	3	1ere_EST_D_600 PDB CREDO	0.605	0.173	0.554	0.005
Rv3133c.1	3	3oll_EST_B_600 PDB CREDO	0.605	0.173	0.554	0.005
Rv3133c.1	15	2jih_097_A_1001 PDB CREDO	0.554	0.239	0.554	0.005
Rv3133c.1	15	3ads_IMN_A_1 PDB CREDO	0.579	0.205	0.550	0.005
Rv3133c.1	3	2y7j_B49_C_1294 PDB CREDO	0.659	0.116	0.545	0.005
Rv3133c.1	1	1hwl_FBI_B_1 PDB CREDO	0.576	0.209	0.543	0.006
Rv3133c.1	1	1hwl_FBI_D_3 PDB CREDO	0.576	0.209	0.543	0.006
Rv3133c.1	1	1hwl_FBI_C_4 PDB CREDO	0.576	0.209	0.543	0.006
Rv3133c.1	1	1hwl_FBI_A_2 PDB CREDO	0.575	0.210	0.542	0.006
Rv3133c.1	3	2y7j_B49_B_1294 PDB CREDO	0.671	0.105	0.542	0.006
Rv3133c.1	1	4asd_BAX_A_1500 PDB CREDO	0.556	0.236	0.540	0.006
Rv3133c.1	1	1uob_PNN_A_1311 PDB CREDO	0.571	0.216	0.538	0.006
Rv3133c.1	3	1mx1_THA_B_2 PDB CREDO	0.638	0.136	0.537	0.006
Rv3133c.1	3	2jj8_AZZ_A_1211 PDB CREDO	0.588	0.194	0.536	0.006
Rv3133c.1	3	2hnd_NVP_A_999 PDB CREDO	0.609	0.168	0.535	0.006
Rv3133c.1	1	1hwk_117_D_3 PDB CREDO	0.582	0.201	0.532	0.007
Rv3133c.1	3	3tmz_06X_A_504 PDB CREDO	0.641	0.133	0.531	0.007
Rv3133c.1	3	1yi4_ADN_A_306 PDB CREDO	0.747	0.050	0.530	0.007
Rv3133c.1	1	1hwi_115_B_1 PDB CREDO	0.617	0.160	0.530	0.007
Rv3133c.1	1	1hwi_115_D_3 PDB CREDO	0.615	0.161	0.529	0.007
Rv3133c.1	3	2x1l_ADN_C_601 PDB CREDO	0.528	0.275	0.528	0.007
Rv3133c.1	3	2fum_MIX_C_2539 PDB CREDO	0.679	0.098	0.527	0.007
Rv3133c.1	3	1mx1_THA_A_1 PDB CREDO	0.600	0.179	0.527	0.007
Rv3133c.1	3	3clb_TMQ_B_612 PDB CREDO	0.551	0.243	0.526	0.007
Rv3133c.1	3	3tbg_RTZ_C_1 PDB CREDO	0.526	0.278	0.526	0.007
Rv3133c.1	1	3hec_STI_A_1 PDB CREDO	0.611	0.166	0.525	0.007
Rv3133c.1	3	1r9o_FLP_A_501 PDB CREDO	0.548	0.247	0.523	0.008
Rv3133c.1	1	1uwj_BAX_A_1723 PDB CREDO	0.554	0.239	0.523	0.008
Rv3133c.1	3	2jj8_AZZ_D_1211 PDB CREDO	0.573	0.213	0.522	0.008
Rv3133c.1	16	1oq5_CEL_A_701 PDB CREDO	0.541	0.256	0.522	0.008
Rv3133c.1	3	1s9p_DES_B_459 PDB CREDO	0.672	0.104	0.522	0.008
Rv3133c.1	3	3qlg_1N1_A_601 PDB CREDO	0.698	0.082	0.521	0.008
Rv3133c.1	3	2jj8_AZZ_C_1211 PDB CREDO	0.569	0.218	0.519	0.008
Rv3133c.1	3	2uxp_CLM_B_1211 PDB CREDO	0.543	0.253	0.519	0.008
Rv3133c.1	3	3b2r_VDN_A_1 PDB CREDO	0.518	0.290	0.518	0.008
Rv3133c.1	15	4dta_ADN_A_401 PDB CREDO	0.658	0.117	0.518	0.008
Rv3133c.1	3	3qlg_1N1_B_601 PDB CREDO	0.694	0.086	0.518	0.008
Rv3133c.1	15	1uay_ADN_A_1001 PDB CREDO	0.628	0.147	0.518	0.008
Rv3133c.1	16	3kw2_ADN_A_300 PDB CREDO	0.537	0.262	0.518	0.008
Rv3133c.1	3	3g5d_1N1_A_1 PDB CREDO	0.693	0.086	0.517	0.008
Rv3133c.1	3	1tbf_VIA_A_501 PDB CREDO	0.541	0.256	0.517	0.008
Rv3133c.1	3	3g5d_1N1_B_1 PDB CREDO	0.692	0.087	0.517	0.008
Rv3133c.1	3	3hp1_LLT_A_401 PDB CREDO	0.516	0.293	0.516	0.009
Rv3133c.1	3	1s9p_DES_C_500 PDB CREDO	0.665	0.111	0.516	0.009
Rv3133c.1	15	3rf4_FUN_C_203 PDB CREDO	0.515	0.295	0.515	0.009
Rv3133c.1	1	1uwj_BAX_B_1723 PDB CREDO	0.530	0.272	0.515	0.009
Rv3133c.1	3	2uxp_CLM_A_1211 PDB CREDO	0.538	0.261	0.514	0.009
Rv3133c.1	3	3b2r_VDN_B_1 PDB CREDO	0.514	0.296	0.514	0.009
Rv3133c.1	3	3grv_ADN_A_300 PDB CREDO	0.564	0.225	0.514	0.009
Rv3133c.1	1	1xkk_FMM_A_91 PDB CREDO	0.657	0.117	0.513	0.009
Rv3133c.1	15	3rf4_FUN_B_202 PDB CREDO	0.513	0.299	0.513	0.009
Rv3133c.1	3	3tbg_RTZ_B_1 PDB CREDO	0.560	0.230	0.511	0.009
Rv3133c.1	1	3heg_BAX_A_1 PDB CREDO	0.542	0.256	0.511	0.009
Rv3133c.1	3	3tbg_RTZ_A_1 PDB CREDO	0.582	0.201	0.511	0.009
Rv3133c.1	16	4eyb_0WO_B_301 PDB CREDO	0.510	0.302	0.510	0.009
Rv3133c.1	15	3rf4_FUN_A_201 PDB CREDO	0.510	0.302	0.510	0.009
Rv3133c.1	3	2vpp_GEO_A_1210 PDB CREDO	0.559	0.231	0.510	0.009
Rv3133c.1	15	1sn0_T44_B_602 PDB CREDO	0.536	0.264	0.509	0.009
Rv3133c.1	3	2jj8_AZZ_B_1211 PDB CREDO	0.557	0.234	0.508	0.010
Rv3133c.1	15	2oa1_ADN_B_2005 PDB CREDO	0.562	0.228	0.506	0.010
Rv3133c.1	3	3fl9_TOP_H_200 PDB CREDO	0.638	0.136	0.503	0.010
Rv3133c.1	3	1g50_EST_A_600 PDB CREDO	0.619	0.157	0.500	0.011

Similarity to known drug target from sensitive sequence analysis

No drug targets

List of small molecules tested from TIBLE

View results in TIBLE page

Name	Affinity	Assay description	DOI
CHEMBL569421	Not Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL569650	Not Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL570135	Not Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL570136	Not Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571036	IC50 = 84.2 ug ml-1	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571036	Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA at 250 uM after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571500	Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA at 250 uM after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571500	IC50 < 26.2 ug ml-1	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571500	Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA added after DevR phosphorylation by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571500	Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA added before DevR phosphorylation by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571501	Not Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571713	Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA at 250 uM after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571713	IC50 = 144.9 ug ml-1	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL571714	Not Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL572150	Not Active	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL583462	Inhibition = 100 %	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA at 500 uM after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833
CHEMBL583462	IC50 = 99 ug ml-1	Inhibition of Mycobacterium tuberculosis phosphorylated DevR binding to fdxA promoter DNA after 10 mins by EMSA	http://www.ncbi.nlm.nih.gov/pubmed/19827833

Off-target activity - ligand based from TIBLE

View results in TIBLE page

Predicted off-target	Method	Summary	Full results
Tyrosine-protein kinase BTK 1B55	PharmMapper	0 hydroph + 9 HB + 3 pos/neg + 0 arom	Link
Neprilysin 1R1H	PharmMapper	3 hydroph + 5 HB + 2 pos/neg + 0 arom	Link
GTPase HRas 1P2S	PharmMapper	0 hydroph + 14 HB + 1 pos/neg + 0 arom	Link
Bifunctional purine biosynthesis protein PURH 1P4R	PharmMapper	0 hydroph + 8 HB + 1 pos/neg + 0 arom	Link
Insulin receptor 1I44	PharmMapper	0 hydroph + 6 HB + 2 pos/neg + 0 arom	Link
Transcription factor STAT3	PASS	Pa = 0.751 & SM = CHEMBL571036	Link
Sonic hedgehog protein	SEA	E_value = 3.71e-30 & MaxTC = 0.43	Link
Matrix metalloproteinase 13	SEA	E_value = 1.21e-18 & MaxTC = 0.41	Link
Prostanoid EP1 receptor	SEA	E_value = 4.4e-16 & MaxTC = 0.37	Link
Liver glycogen phosphorylase	SEA	E_value = 1.97e-13 & MaxTC = 0.48	Link
Phosphodiesterase 4A	SEA	E_value = 4.93e-13 & MaxTC = 0.42	Link
capsaicin receptor; vanilloid receptor	SEA	E_value = 1.45e-12 & MaxTC = 0.41	Link

Small molecules involved in protein-protein complex from TIMBAL .Proteins similar to Mtb based on sequence analysis.

Data not available

STITCH interactions

Chemical Name	Confidence score	Molecular Weight
selenomethioninePubChem	0.934	196.106
SeMetPubChem	0.919	196.106
hydron sulfatePubChem	0.913	196.157
sulfatePubChem	0.913	96.0626
compound 10PubChem	0.864	231.721