SInCRe - Rv1612

Tuberculist information

Gene name	trpB
Protein function	Tryptophan synthase, beta subunit TrpB
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	1811.13
Molecular mass(da)	43286.7
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 410

	  		  	1    MSAAIAEPTSHDPDSGGHFGGPSGWGGRYVPEALMAVIEEVTAAYQKERVSQDFLDDLDR   60
			  	61   LQANYAGRPSPLYEATRLSQHAGSARIFLKREDLNHTGSHKINNVLGQALLARRMGKTRV  120
			  	121  IAETGAGQHGVATATACALLGLDCVIYMGGIDTARQALNVARMRLLGAEVVAVQTGSKTL  180
			  	181  KDAINEAFRDWVANADNTYYCFGTAAGPHPFPTMVRDFQRIIGMEARVQIQGQAGRLPDA  240
			  	241  VVACVGGGSNAIGIFHAFLDDPGVRLVGFEAAGDGVETGRHAATFTAGSPGAFHGSFSYL  300
			  	301  LQDEDGQTIESHSISAGLDYPGVGPEHAWLKEAGRVDYRPITDSEAMDAFGLLCRMEGII  360
			  	361  PAIESAHAVAGALKLGVELGRGAVIVVNLSGRGDKDVETAAKWFGLLGND

Known structures in the PDB

	PDB ID	2O2E
	Total residue count	844
	Number of chains	2
	Method	X-RAY
	Resolution	2.2

	PDB ID	2O2J
	Total residue count	844
	Number of chains	2
	Method	X-RAY
	Resolution	2.56

Number of amino acids : 410

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
PALP	PF00291	75-403

Mtb Structural Proteome models

Model Number	1
Model name	Rv1612_2o2e_A
Template	2O2E APDB CREDO
Template coverage	29_404
Template Identity(%)	100.0
Model coverage(%)	91.5
Normalized DOPE score	-1.221

Model Number	2
Model name	Rv1612
Template	1V8Z APDB CREDO
Template coverage	3_386
Template Identity(%)	58.1
Model coverage(%)	93.4
Normalized DOPE score	-1.093

Structure Models from Chopin

Model Number	1
Profile	c.79.1.1 Click for model details
zscore	29.03
Residue begin	1
Residue end	410

Model Number	2
Profile	3.40.50.1100 Click for model details
zscore	15.07
Residue begin	155
Residue end	407

Binding pockets

STRING

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

Protein interacting with Rv1612	Gene name	Confidence Score
Rv1611	trpC	0.999
Rv1613	trpA	0.999
Rv2192c	trpD	0.998
Rv2192c	trpD	0.998
Rv1609	trpE	0.997
Rv1609	trpE	0.997
Rv3336c	trpS	0.989
Rv0013	trpG	0.984
Rv0070c	glyA2	0.98
Rv1093	glyA1	0.979
Rv2540c	aroF	0.978
Rv1559	ilvA	0.964
Rv1559	ilvA	0.964
Rv3042c	serB2	0.964
Rv3042c	serB2	0.964
Rv1602	hisH	0.957
Rv1605	hisF	0.955
Rv3455c	truA	0.954
Rv2537c	aroD	0.949
Rv2335	cysE	0.948
Rv2335	cysE	0.948
Rv1601	hisB	0.948
Rv2538c	aroB	0.942
Rv2121c	hisG	0.938
Rv2121c	hisG	0.938
Rv1603	hisA	0.938
Rv2447c	folC	0.934
Rv2447c	folC	0.934
Rv1599	hisD	0.934
Rv3838c	pheA	0.934
Rv1077	cbs	0.934
Rv3838c	pheA	0.934
Rv1077	cbs	0.934
Rv3227	aroA	0.927
Rv0189c	ilvD	0.922
Rv2995c	leuB	0.918
Rv2614c	thrS	0.915
Rv2614c	thrS	0.915
Rv2614c	thrS	0.915
Rv1617	pykA	0.913
Rv1617	pykA	0.913
Rv1606	hisI	0.913
Rv2483c	plsC	0.913
Rv2483c	plsC	0.913
Rv3708c	asd	0.904
Rv3708c	asd	0.904
Rv3003c	ilvB1	0.901
Rv3003c	ilvB1	0.901
Rv3003c	ilvB1	0.901

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv1612_2o2e_A	18	1gsf_EAA_A_223 PDB CREDO	0.657	0.117	0.657	0.001
Rv1612_2o2e_A	18	1gsf_EAA_B_223 PDB CREDO	0.657	0.117	0.657	0.001
Rv1612_2o2e_A	18	1gsf_EAA_C_223 PDB CREDO	0.657	0.117	0.657	0.001
Rv1612_2o2e_A	18	1gsf_EAA_D_223 PDB CREDO	0.657	0.117	0.657	0.001
Rv1612_2o2e_A	18	1ikv_EFZ_A_2000 PDB CREDO	0.690	0.089	0.655	0.001
Rv1612_2o2e_A	18	1gse_EAA_B_224 PDB CREDO	0.677	0.099	0.610	0.002
Rv1612_2o2e_A	18	1gse_EAA_A_224 PDB CREDO	0.676	0.101	0.609	0.002
Rv1612_2o2e_A	18	3uqb_FK5_A_114 PDB CREDO	0.659	0.116	0.590	0.003
Rv1612_2o2e_A	18	2ipg_FFA_A_3 PDB CREDO	0.613	0.164	0.580	0.003
Rv1612_2o2e_A	18	1ikw_EFZ_A_2000 PDB CREDO	0.701	0.080	0.573	0.003
Rv1612_2o2e_A	18	3p4w_DSF_D_319 PDB CREDO	0.666	0.110	0.563	0.004
Rv1612_2o2e_A	18	3jwq_VIA_C_901 PDB CREDO	0.624	0.151	0.563	0.004
Rv1612_2o2e_A	18	3p4w_DSF_B_319 PDB CREDO	0.662	0.113	0.560	0.004
Rv1612_2o2e_A	18	3p4w_DSF_E_319 PDB CREDO	0.662	0.113	0.560	0.004
Rv1612_2o2e_A	18	1vrt_NVP_A_999 PDB CREDO	0.777	0.034	0.552	0.005
Rv1612_2o2e_A	18	1z11_8MO_B_501 PDB CREDO	0.579	0.205	0.549	0.005
Rv1612_2o2e_A	18	3jwq_VIA_A_901 PDB CREDO	0.579	0.205	0.549	0.005
Rv1612_2o2e_A	18	1y7i_SAL_A_501 PDB CREDO	0.610	0.168	0.546	0.005
Rv1612_2o2e_A	18	1y7i_SAL_B_503 PDB CREDO	0.610	0.168	0.546	0.005
Rv1612_2o2e_A	18	1lwe_NVP_A_999 PDB CREDO	0.767	0.039	0.544	0.005
Rv1612_2o2e_A	18	1q6i_FK5_A_301 PDB CREDO	0.541	0.257	0.541	0.006
Rv1612_2o2e_A	18	1s1x_NVP_A_999 PDB CREDO	0.758	0.043	0.538	0.006
Rv1612_2o2e_A	18	2ipf_FFA_B_4 PDB CREDO	0.538	0.261	0.538	0.006
Rv1612_2o2e_A	18	2ipf_FFA_A_3 PDB CREDO	0.533	0.268	0.533	0.007
Rv1612_2o2e_A	16	2w9s_TOP_B_1160 PDB CREDO	0.533	0.268	0.533	0.007
Rv1612_2o2e_A	18	1cqp_803_B_311 PDB CREDO	0.717	0.068	0.533	0.007
Rv1612_2o2e_A	18	3pgh_FLP_C_701 PDB CREDO	0.717	0.068	0.533	0.007
Rv1612_2o2e_A	18	3n8y_DIF_B_585 PDB CREDO	0.681	0.096	0.530	0.007
Rv1612_2o2e_A	18	1wrl_TFP_E_212 PDB CREDO	0.556	0.236	0.526	0.007
Rv1612_2o2e_A	18	3f8f_DM1_A_127 PDB CREDO	0.553	0.240	0.523	0.008
Rv1612_2o2e_A	16	1fdw_EST_A_350 PDB CREDO	0.523	0.284	0.523	0.008
Rv1612_2o2e_A	18	1tbf_VIA_A_501 PDB CREDO	0.700	0.081	0.520	0.008
Rv1612_2o2e_A	16	3qfx_CP6_B_702 PDB CREDO	0.520	0.288	0.520	0.008
Rv1612_2o2e_A	18	2efj_37T_A_502 PDB CREDO	0.666	0.110	0.518	0.008
Rv1612_2o2e_A	18	2bxq_IMN_A_2001 PDB CREDO	0.575	0.211	0.518	0.008
Rv1612_2o2e_A	16	3qfx_CP6_A_602 PDB CREDO	0.515	0.295	0.515	0.009
Rv1612_2o2e_A	18	3hgx_SAL_B_104 PDB CREDO	0.542	0.255	0.514	0.009
Rv1612_2o2e_A	18	2w98_P1Z_B_1356 PDB CREDO	0.541	0.257	0.512	0.009
Rv1612_2o2e_A	18	3ret_SAL_B_201 PDB CREDO	0.539	0.260	0.511	0.009
Rv1612_2o2e_A	18	1lwc_NVP_A_999 PDB CREDO	0.818	0.019	0.510	0.009
Rv1612_2o2e_A	18	4cox_IMN_D_701 PDB CREDO	0.686	0.092	0.510	0.009
Rv1612_2o2e_A	18	1q6i_FK5_B_401 PDB CREDO	0.593	0.187	0.509	0.010
Rv1612_2o2e_A	18	3qip_NVP_A_561 PDB CREDO	0.815	0.020	0.508	0.010
Rv1612_2o2e_A	18	1fdu_EST_D_352 PDB CREDO	0.563	0.226	0.508	0.010
Rv1612_2o2e_A	16	3gvu_STI_A_1002 PDB CREDO	0.508	0.307	0.508	0.010
Rv1612_2o2e_A	18	1juj_LYA_D_315 PDB CREDO	0.535	0.266	0.507	0.010
Rv1612_2o2e_A	18	2ipg_FFA_B_4 PDB CREDO	0.598	0.181	0.506	0.010
Rv1612_2o2e_A	18	1lwf_NVP_A_999 PDB CREDO	0.812	0.021	0.506	0.010
Rv1612_2o2e_A	18	1juj_LYA_A_315 PDB CREDO	0.533	0.268	0.506	0.010
Rv1612_2o2e_A	18	1juj_LYA_B_315 PDB CREDO	0.533	0.268	0.506	0.010
Rv1612_2o2e_A	18	1juj_LYA_C_315 PDB CREDO	0.533	0.268	0.506	0.010
Rv1612_2o2e_A	4	2ex6_AIC_A_501 PDB CREDO	0.506	0.309	0.506	0.010
Rv1612_2o2e_A	16	3fl9_TOP_C_200 PDB CREDO	0.533	0.268	0.505	0.010
Rv1612_2o2e_A	16	3mdt_VOR_B_506 PDB CREDO	0.533	0.268	0.505	0.010
Rv1612_2o2e_A	16	2w98_P1Z_A_1353 PDB CREDO	0.533	0.268	0.505	0.010
Rv1612_2o2e_A	18	2hny_NVP_A_999 PDB CREDO	0.808	0.022	0.504	0.010
Rv1612_2o2e_A	18	3lp0_NVP_A_701 PDB CREDO	0.807	0.022	0.503	0.010
Rv1612_2o2e_A	18	2y7p_SAL_A_1000 PDB CREDO	0.560	0.230	0.502	0.011
Rv1612_2o2e_A	18	3ret_SAL_A_201 PDB CREDO	0.530	0.273	0.502	0.011
Rv1612_2o2e_A	18	3uqa_FK5_A_114 PDB CREDO	0.502	0.315	0.502	0.011
Rv1612_2o2e_A	18	2hnd_NVP_A_999 PDB CREDO	0.805	0.023	0.502	0.011
Rv1612_2o2e_A	16	2w9g_TOP_A_1159 PDB CREDO	0.502	0.316	0.502	0.011
Rv1612_2o2e_A	16	3mdt_VOR_A_506 PDB CREDO	0.529	0.275	0.501	0.011
Rv1612_2o2e_A	16	3fl9_TOP_G_200 PDB CREDO	0.557	0.234	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
indole-3-glycerol phosphatePubChem	0.992	287.206
indolePubChem	0.984	117.148
L-serinePubChem	0.982	105.093
D-glyceraldehyde-3-phosphatePubChem	0.98	170.058
pyridoxal phosphatePubChem	0.947	247.142
L-tryptophanPubChem	0.945	204.225
DL-serinePubChem	0.9	105.093
IGPSPubChem	0.9	287.206
glyceraldehyde-3-phosphatePubChem	0.9	170.058
hydroxyl radicalsPubChem	0.9	17.0073
Na(+)PubChem	0.835	22.9898
Tn5PubChem	0.732	270.111
anthranilic acidPubChem	0.727	137.136
sulfatePubChem	0.712	96.0626
SeMetPubChem	0.708	196.106
selenomethioninePubChem	0.708	196.106
chloridePubChem	0.708	35.453
indolinePubChem	0.701	119.164
glycerol-3-phosphatePubChem	0.701	172.074
P1TPubChem	0.701	318.22
NHPPubChem	0.701	261.278
CsClPubChem	0.701	168.358
2cllPubChem	0.701	365.22
1cw2PubChem	0.701	278.262
IAGPubChem	0.701	232.235
5-fluoroindole propanol phosphatePubChem	0.701	273.197
dimethyl sulphoxidePubChem	0.701	78.1334
1tjpPubChem	0.701	279.184
HpfPubChem	0.701	279.184
indole-3-propanol phosphatePubChem	0.701	255.207
glycerolPubChem	0.701	92.0938
f19PubChem	0.701	331.281
CHEBI:58866PubChem	0.701	285.19
2CLMPubChem	0.701	329.166
DB07894PubChem	0.701	278.237
indole-3-acetyl-l-aspartic acidPubChem	0.701	290.271
potassiumPubChem	0.701	39.0983
potassium hydridePubChem	0.701	40.1062
1C29PubChem	0.701	260.247
dihydroxyacetone phosphatePubChem	0.701	170.058
indole-3-acetyl-l-valinePubChem	0.701	274.315
PLP-SerPubChem	0.701	336.235
KouPubChem	0.701	336.235
hydron sulfatePubChem	0.701	196.157