SInCRe - Rv3646c

Tuberculist information

Gene name	topA
Protein function	DNA topoisomerase I TopA (omega-protein) (relaxing enzyme) (untwisting enzyme) (swivelase) (type I DNA topoisomerase) (nicking-closing enzyme) (TOPO I)
Functional category(tuberculist)	information pathways
Gene location(kb)	4084.45
Molecular mass(da)	102318
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 934

	  		  	1    LADPKTKGRGSGGNGSGRRLVIVESPTKARKLASYLGSGYIVESSRGHIRDLPRAASDVP   60
			  	61   AKYKSQPWARLGVNVDADFEPLYIISPEKRSTVSELRGLLKDVDELYLATDGDREGEAIA  120
			  	121  WHLLETLKPRIPVKRMVFHEITEPAIRAAAEHPRDLDIDLVDAQETRRILDRLYGYEVSP  180
			  	181  VLWKKVAPKLSAGRVQSVATRIIVARERDRMAFRSAAYWDILAKLDASVSDPDAAPPTFS  240
			  	241  ARLTAVAGRRVATGRDFDSLGTLRKGDEVIVLDEGSATALAAGLDGTQLTVASAEEKPYA  300
			  	301  RRPYPPFMTSTLQQEASRKLRFSAERTMSIAQRLYENGYITYMRTDSTTLSESAINAART  360
			  	361  QARQLYGDEYVAPAPRQYTRKVKNAQEAHEAIRPAGETFATPDAVRRELDGPNIDDFRLY  420
			  	421  ELIWQRTVASQMADARGMTLSLRITGMSGHQEVVFSATGRTLTFPGFLKAYVETVDELVG  480
			  	481  GEADDAERRLPHLTPGQRLDIVELTPDGHATNPPARYTEASLVKALEELGIGRPSTYSSI  540
			  	541  IKTIQDRGYVHKKGSALVPSWVAFAVTGLLEQHFGRLVDYDFTAAMEDELDEIAAGNERR  600
			  	601  TNWLNNFYFGGDHGVPDSVARSGGLKKLVGINLEGIDAREVNSIKLFDDTHGRPIYVRVG  660
			  	661  KNGPYLERLVAGDTGEPTPQRANLSDSITPDELTLQVAEELFATPQQGRTLGLDPETGHE  720
			  	721  IVAREGRFGPYVTEILPEPAADAAAAAQGVKKRQKAAGPKPRTGSLLRSMDLQTVTLEDA  780
			  	781  LRLLSLPRVVGVDPASGEEITAQNGRYGPYLKRGNDSRSLVTEDQIFTITLDEALKIYAE  840
			  	841  PKRRGRQSASAPPLRELGTDPASGKPMVIKDGRFGPYVTDGETNASLRKGDDVASITDER  900
			  	901  AAELLADRRARGPAKRPARKAARKVPAKKAAKRD

Known structures in the PDB

No Known structures

Number of amino acids : 934

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
Toprim	PF01751	19-141
Topoisom_bac	PF01131	155-605
Toprim_C_rpt	PF13368	714-791
Toprim_C_rpt	PF13368	793-853
Toprim_C_rpt	PF13368	860-924

Mtb Structural Proteome models

Model Number	1
Model name	Rv3646c
Template	1MW9 XPDB CREDO
Template coverage	2_592
Template Identity(%)	44.1
Model coverage(%)	65.6
Normalized DOPE score	0.009

Model Number	2
Model name	Rv3646c.2
Template	2GAI APDB CREDO
Template coverage	7_598
Template Identity(%)	37.5
Model coverage(%)	71.6
Normalized DOPE score	0.228

Structure Models from Chopin

Model Number	1
Profile	e.10.1.1 Click for model details
zscore	58.71
Residue begin	155
Residue end	605

Model Number	2
Profile	1.10.460.10 Click for model details
zscore	34.21
Residue begin	458
Residue end	605

Model Number	3
Profile	e.10.1.1 Click for model details
zscore	29.12
Residue begin	19
Residue end	141

Model Number	4
Profile	1.10.290.10 Click for model details
zscore	21.98
Residue begin	304
Residue end	429

Binding pockets

STRING

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

Protein interacting with Rv3646c	Gene name	Confidence Score
Rv1701	Rv1701	0.972
Rv1701	Rv1701	0.972
Rv0005	gyrB	0.964
Rv0005	gyrB	0.964
Rv0005	gyrB	0.964
Rv0005	gyrB	0.964
Rv0668	rpoC	0.942
Rv0668	rpoC	0.942
Rv0668	rpoC	0.942
Rv0668	rpoC	0.942
Rv0668	rpoC	0.942
Rv0054	ssb	0.937
Rv2894c	xerC	0.935
Rv2894c	xerC	0.935
Rv3457c	rpoA	0.927
Rv3457c	rpoA	0.927
Rv3457c	rpoA	0.927
Rv0006	gyrA	0.926
Rv0006	gyrA	0.926
Rv2906c	trmD	0.925
Rv2916c	ffh	0.923
Rv2916c	ffh	0.923
Rv2916c	ffh	0.923
Rv0667	rpoB	0.922
Rv0667	rpoB	0.922
Rv0667	rpoB	0.922
Rv0667	rpoB	0.922
Rv0667	rpoB	0.922
Rv0667	rpoB	0.922
Rv1629	polA	0.917
Rv1629	polA	0.917
Rv1629	polA	0.917
Rv2462c	tig	0.915
Rv2462c	tig	0.915
Rv2462c	tig	0.915
Rv2737c	recA	0.91
Rv2737c	recA	0.91
Rv2748c	ftsK	0.907
Rv2748c	ftsK	0.907
Rv2748c	ftsK	0.907
Rv2150c	ftsZ	0.905
Rv2150c	ftsZ	0.905
Rv2889c	tsf	0.901
Rv2889c	tsf	0.901

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv3646c.2	7	1uwj_BAX_A_1723 PDB CREDO	0.577	0.208	0.561	0.004
Rv3646c.2	47	1hwk_117_D_3 PDB CREDO	0.559	0.232	0.559	0.004
Rv3646c.2	19	3tne_RIT_B_401 PDB CREDO	0.695	0.085	0.548	0.005
Rv3646c.2	7	3tne_RIT_B_401 PDB CREDO	0.653	0.121	0.545	0.005
Rv3646c.2	7	4asd_BAX_A_1500 PDB CREDO	0.575	0.210	0.542	0.006
Rv3646c.2	47	1hwk_117_A_2 PDB CREDO	0.575	0.210	0.542	0.006
Rv3646c.2	47	1hwl_FBI_A_2 PDB CREDO	0.557	0.235	0.540	0.006
Rv3646c.2	47	1hwl_FBI_C_4 PDB CREDO	0.557	0.235	0.540	0.006
Rv3646c.2	47	1hwk_117_C_4 PDB CREDO	0.572	0.214	0.539	0.006
Rv3646c.2	14	1hwk_117_B_1 PDB CREDO	0.687	0.091	0.538	0.006
Rv3646c.2	7	1uwj_BAX_B_1723 PDB CREDO	0.568	0.219	0.536	0.006
Rv3646c.2	19	1uwj_BAX_A_1723 PDB CREDO	0.549	0.245	0.534	0.006
Rv3646c.2	47	1hwl_FBI_D_3 PDB CREDO	0.550	0.244	0.533	0.007
Rv3646c.2	14	1hwk_117_A_2 PDB CREDO	0.721	0.066	0.533	0.007
Rv3646c.2	14	1hwk_117_C_4 PDB CREDO	0.720	0.066	0.532	0.007
Rv3646c.2	47	1hwl_FBI_B_1 PDB CREDO	0.547	0.248	0.531	0.007
Rv3646c.2	7	3pyy_STI_A_3 PDB CREDO	0.530	0.273	0.530	0.007
Rv3646c.2	19	3pww_ROC_A_1001 PDB CREDO	0.588	0.193	0.528	0.007
Rv3646c.2	7	3pyy_STI_B_4 PDB CREDO	0.525	0.280	0.525	0.007
Rv3646c.2	19	3tne_RIT_A_401 PDB CREDO	0.664	0.111	0.524	0.008
Rv3646c.2	7	2hyy_STI_A_600 PDB CREDO	0.523	0.284	0.523	0.008
Rv3646c.2	7	1iep_STI_A_201 PDB CREDO	0.522	0.284	0.522	0.008
Rv3646c.2	7	3tne_RIT_A_401 PDB CREDO	0.625	0.150	0.522	0.008
Rv3646c.2	7	1t46_STI_A_3 PDB CREDO	0.615	0.161	0.521	0.008
Rv3646c.2	7	1iep_STI_B_202 PDB CREDO	0.520	0.287	0.520	0.008
Rv3646c.2	7	3mss_STI_D_1 PDB CREDO	0.520	0.287	0.520	0.008
Rv3646c.2	7	3ms9_STI_B_1 PDB CREDO	0.520	0.288	0.520	0.008
Rv3646c.2	7	2hyy_STI_D_600 PDB CREDO	0.519	0.289	0.519	0.008
Rv3646c.2	7	3gvu_STI_A_1001 PDB CREDO	0.519	0.289	0.519	0.008
Rv3646c.2	7	3mss_STI_C_1 PDB CREDO	0.519	0.289	0.519	0.008
Rv3646c.2	7	1hwk_117_B_1 PDB CREDO	0.519	0.289	0.519	0.008
Rv3646c.2	7	3mss_STI_A_1 PDB CREDO	0.519	0.289	0.519	0.008
Rv3646c.2	19	3q70_RIT_A_2001 PDB CREDO	0.599	0.180	0.518	0.008
Rv3646c.2	7	3k5v_STI_B_2 PDB CREDO	0.518	0.291	0.518	0.008
Rv3646c.2	7	3mss_STI_B_1 PDB CREDO	0.518	0.291	0.518	0.008
Rv3646c.2	7	3ms9_STI_A_1 PDB CREDO	0.517	0.292	0.517	0.008
Rv3646c.2	7	1uwh_BAX_B_1723 PDB CREDO	0.581	0.203	0.516	0.009
Rv3646c.2	7	1uwh_BAX_A_1723 PDB CREDO	0.580	0.203	0.516	0.009
Rv3646c.2	7	2hyy_STI_C_600 PDB CREDO	0.516	0.294	0.516	0.009
Rv3646c.2	14	1hwk_117_D_3 PDB CREDO	0.740	0.053	0.515	0.009
Rv3646c.2	14	1hwl_FBI_C_4 PDB CREDO	0.717	0.068	0.514	0.009
Rv3646c.2	7	3oez_STI_A_601 PDB CREDO	0.514	0.296	0.514	0.009
Rv3646c.2	14	1hwl_FBI_B_1 PDB CREDO	0.716	0.069	0.514	0.009
Rv3646c.2	14	1hwl_FBI_A_2 PDB CREDO	0.715	0.070	0.513	0.009
Rv3646c.2	14	1hwl_FBI_D_3 PDB CREDO	0.715	0.070	0.513	0.009
Rv3646c.2	19	2vn1_FK5_A_501 PDB CREDO	0.527	0.278	0.512	0.009
Rv3646c.2	19	3d91_REM_A_350 PDB CREDO	0.573	0.212	0.511	0.009
Rv3646c.2	47	1hwk_117_B_1 PDB CREDO	0.574	0.211	0.510	0.009
Rv3646c.2	19	3d91_REM_B_350 PDB CREDO	0.570	0.217	0.508	0.010
Rv3646c.2	47	1hwi_115_B_1 PDB CREDO	0.540	0.258	0.508	0.010
Rv3646c.2	47	1hwi_115_D_3 PDB CREDO	0.540	0.258	0.508	0.010
Rv3646c.2	7	2y6o_1N1_A_1892 PDB CREDO	0.626	0.149	0.506	0.010
Rv3646c.2	19	1uwj_BAX_B_1723 PDB CREDO	0.564	0.225	0.503	0.010
Rv3646c.2	7	2hyy_STI_B_600 PDB CREDO	0.549	0.246	0.502	0.011
Rv3646c.2	8	1hwk_117_B_1 PDB CREDO	0.776	0.035	0.501	0.011

Similarity to known drug target from sensitive sequence analysis

No drug targets

List of small molecules tested from TIBLE

Data not available

Off-target activity - ligand based from TIBLE

Data not available

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
BE-10988PubChem	0.795	302.309
zincPubChem	0.719	65.409
trioctylphosphine oxidePubChem	0.716	386.635
phosphatePubChem	0.707	96.9872
2,4,5-trihydroxyphenylalanine quinonePubChem	0.706	211.171
topa quinonePubChem	0.703	211.171
novobiocinPubChem	0.701	611.616