SInCRe - Rv3330

Tuberculist information

Gene name	dacB1
Protein function	Probable penicillin-binding protein DacB1 (D-alanyl-D-alanine carboxypeptidase) (DD-peptidase) (DD-carboxypeptidase) (PBP) (DD-transpeptidase) (serine-type D-ala-D-ala carboxypeptidase) (D-amino acid hydrolase)
Functional category(tuberculist)	cell wall and cell processes
Gene location(kb)	3715.78
Molecular mass(da)	41682.3
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 405

	  		  	1    MAFLRSVSCLAAAVFAVGTGIGLPTAAGEPNAAPAACPYKVSTPPAVDSSEVPAAGEPPL   60
			  	61   PLVVPPTPVGGNALGGCGIITAPGSAPAPGDVSAEAWLVADLDSGAVIAARDPHGRHRPA  120
			  	121  SVIKVLVAMASINTLTLNKSVAGTADDAAVEGTKVGVNTGGTYTVNQLLHGLLMHSGNDA  180
			  	181  AYALARQLGGMPAALEKINLLAAKLGGRDTRVATPSGLDGPGMSTSAYDIGLFYRYAWQN  240
			  	241  PVFADIVATRTFDFPGHGDHPGYELENDNQLLYNYPGALGGKTGYTDDAGQTFVGAANRD  300
			  	301  GRRLMTVLLHGTRQPIPPWEQAAHLLDYGFNTPAGTQIGTLIEPDPSLMSTDRNPADRQR  360
			  	361  VDPQAAARISAADALPVRVGVAVIGALIVFGLIMVARAMNRRPQH

Known structures in the PDB

No Known structures

Number of amino acids : 405

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
Peptidase_S11	PF00768	82-313

Mtb Structural Proteome models

Model Number	1
Model name	Rv3330
Template	2BCF APDB CREDO
Template coverage	29_291
Template Identity(%)	46.4
Model coverage(%)	64.4
Normalized DOPE score	-1.216

Model Number	2
Model name	Rv3330.1
Template	1TVF APDB CREDO
Template coverage	16_320
Template Identity(%)	19.5
Model coverage(%)	71.9
Normalized DOPE score	-0.065

Model Number	3
Model name	Rv3330.3
Template	1Z6F APDB CREDO
Template coverage	10_345
Template Identity(%)	25.6
Model coverage(%)	78.0
Normalized DOPE score	0.169

Structure Models from Chopin

Model Number	1
Profile	e.3.1.1 - 3.40.710.10 Click for model details
zscore	8.63
Residue begin	14
Residue end	402

Binding pockets

STRING

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

Protein interacting with Rv3330	Gene name	Confidence Score
Rv2153c	murG	0.914
Rv2153c	murG	0.914

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv3330.1	6	1jlb_NVP_A_999 PDB CREDO	0.652	0.122	0.623	0.001
Rv3330.1	6	3pgh_FLP_C_701 PDB CREDO	0.619	0.156	0.619	0.001
Rv3330.1	6	1lwe_NVP_A_999 PDB CREDO	0.642	0.133	0.613	0.002
Rv3330.1	6	1s1x_NVP_A_999 PDB CREDO	0.638	0.136	0.610	0.002
Rv3330.1	6	1tbf_VIA_A_501 PDB CREDO	0.607	0.171	0.607	0.002
Rv3330.1	6	1vrt_NVP_A_999 PDB CREDO	0.629	0.146	0.601	0.002
Rv3330.1	6	3b2r_VDN_B_1 PDB CREDO	0.623	0.153	0.595	0.002
Rv3330.1	6	3b2r_VDN_A_1 PDB CREDO	0.622	0.154	0.594	0.002
Rv3330.1	6	3pgh_FLP_B_701 PDB CREDO	0.593	0.187	0.593	0.002
Rv3330.1	6	1lwf_NVP_A_999 PDB CREDO	0.699	0.082	0.586	0.003
Rv3330.1	6	1eqg_IBP_B_1701 PDB CREDO	0.580	0.203	0.580	0.003
Rv3330.1	6	1fko_EFZ_A_999 PDB CREDO	0.691	0.087	0.580	0.003
Rv3330.1	6	3lp0_NVP_A_701 PDB CREDO	0.691	0.087	0.580	0.003
Rv3330.1	6	1ikw_EFZ_A_2000 PDB CREDO	0.635	0.139	0.578	0.003
Rv3330.1	6	1gse_EAA_B_224 PDB CREDO	0.700	0.081	0.577	0.003
Rv3330.1	6	1jlf_NVP_A_999 PDB CREDO	0.604	0.175	0.577	0.003
Rv3330.1	6	1eqg_IBP_A_701 PDB CREDO	0.576	0.209	0.576	0.003
Rv3330.1	6	3pgh_FLP_A_701 PDB CREDO	0.576	0.209	0.576	0.003
Rv3330.1	6	3lp1_NVP_A_701 PDB CREDO	0.685	0.093	0.574	0.003
Rv3330.1	6	1lwc_NVP_A_999 PDB CREDO	0.684	0.094	0.574	0.003
Rv3330.1	6	2hny_NVP_A_999 PDB CREDO	0.684	0.094	0.574	0.003
Rv3330.1	6	3qip_NVP_A_561 PDB CREDO	0.683	0.095	0.573	0.003
Rv3330.1	6	1gse_EAA_A_224 PDB CREDO	0.692	0.087	0.571	0.004
Rv3330.1	6	3n8y_DIF_B_585 PDB CREDO	0.595	0.185	0.568	0.004
Rv3330.1	6	1cqe_FLP_A_1650 PDB CREDO	0.641	0.134	0.561	0.004
Rv3330.1	6	1cqe_FLP_B_2650 PDB CREDO	0.641	0.134	0.561	0.004
Rv3330.1	6	2bxp_P1Z_A_3001 PDB CREDO	0.587	0.195	0.560	0.004
Rv3330.1	6	4cox_IMN_D_701 PDB CREDO	0.560	0.230	0.560	0.004
Rv3330.1	6	3pgh_FLP_D_701 PDB CREDO	0.640	0.135	0.560	0.004
Rv3330.1	6	1eqh_FLP_A_701 PDB CREDO	0.636	0.138	0.557	0.004
Rv3330.1	6	1jkh_EFZ_A_999 PDB CREDO	0.664	0.111	0.557	0.004
Rv3330.1	3	1hwk_117_C_4 PDB CREDO	0.557	0.235	0.557	0.004
Rv3330.1	6	2uxp_CLM_A_1211 PDB CREDO	0.554	0.239	0.554	0.005
Rv3330.1	3	1hwk_117_A_2 PDB CREDO	0.554	0.239	0.554	0.005
Rv3330.1	6	1eqh_FLP_B_1701 PDB CREDO	0.632	0.143	0.553	0.005
Rv3330.1	6	1xoz_CIA_A_501 PDB CREDO	0.552	0.241	0.552	0.005
Rv3330.1	6	1s1u_NVP_A_999 PDB CREDO	0.658	0.117	0.551	0.005
Rv3330.1	6	2uxp_CLM_B_1211 PDB CREDO	0.551	0.243	0.551	0.005
Rv3330.1	3	1hwl_FBI_A_2 PDB CREDO	0.565	0.223	0.549	0.005
Rv3330.1	6	1xp0_VDN_A_201 PDB CREDO	0.627	0.148	0.549	0.005
Rv3330.1	3	1hwl_FBI_C_4 PDB CREDO	0.565	0.224	0.548	0.005
Rv3330.3	3	1hwk_117_D_3 PDB CREDO	0.565	0.223	0.548	0.005
Rv3330.1	3	1hwl_FBI_B_1 PDB CREDO	0.564	0.224	0.548	0.005
Rv3330.1	3	1hwl_FBI_D_3 PDB CREDO	0.564	0.225	0.547	0.005
Rv3330.1	6	1udt_VIA_A_1000 PDB CREDO	0.572	0.214	0.546	0.005
Rv3330.1	3	1uob_PNN_A_1311 PDB CREDO	0.562	0.227	0.546	0.005
Rv3330.1	6	3hm1_J3Z_A_2 PDB CREDO	0.545	0.250	0.545	0.005
Rv3330.1	6	3rem_SAL_A_301 PDB CREDO	0.662	0.113	0.545	0.005
Rv3330.1	6	3rem_SAL_B_301 PDB CREDO	0.662	0.113	0.545	0.005
Rv3330.1	6	3axz_ADN_A_401 PDB CREDO	0.595	0.185	0.544	0.006
Rv3330.1	3	1hwk_117_D_3 PDB CREDO	0.577	0.207	0.543	0.006
Rv3330.1	6	4cox_IMN_B_701 PDB CREDO	0.621	0.155	0.543	0.006
Rv3330.1	6	4cox_IMN_C_701 PDB CREDO	0.618	0.158	0.541	0.006
Rv3330.1	6	1fkp_NVP_A_999 PDB CREDO	0.645	0.130	0.541	0.006
Rv3330.1	6	3n8w_FLP_A_701 PDB CREDO	0.623	0.152	0.540	0.006
Rv3330.1	6	3s7s_EXM_A_601 PDB CREDO	0.566	0.222	0.540	0.006
Rv3330.1	6	4cox_IMN_A_701 PDB CREDO	0.616	0.160	0.539	0.006
Rv3330.1	6	1cqp_803_B_311 PDB CREDO	0.539	0.259	0.539	0.006
Rv3330.1	6	3hvt_NVP_A_557 PDB CREDO	0.641	0.134	0.537	0.006
Rv3330.1	6	3vkx_T3_A_301 PDB CREDO	0.589	0.193	0.536	0.006
Rv3330.1	3	3d91_REM_A_350 PDB CREDO	0.536	0.265	0.536	0.006
Rv3330.1	6	2hnd_NVP_A_999 PDB CREDO	0.638	0.136	0.535	0.006
Rv3330.1	3	1hwk_117_B_1 PDB CREDO	0.568	0.220	0.535	0.006
Rv3330.1	6	1ere_EST_B_600 PDB CREDO	0.534	0.267	0.534	0.006
Rv3330.1	3	1z2b_VLB_C_800 PDB CREDO	0.550	0.244	0.534	0.006
Rv3330.1	6	1ere_EST_A_600 PDB CREDO	0.533	0.269	0.533	0.007
Rv3330.1	6	1ikv_EFZ_A_2000 PDB CREDO	0.680	0.097	0.533	0.007
Rv3330.1	3	3d91_REM_B_350 PDB CREDO	0.532	0.270	0.532	0.007
Rv3330.1	6	3jwq_VIA_C_901 PDB CREDO	0.644	0.131	0.531	0.007
Rv3330.1	6	1ere_EST_E_600 PDB CREDO	0.529	0.275	0.529	0.007
Rv3330.1	6	1gwr_EST_A_600 PDB CREDO	0.527	0.276	0.527	0.007
Rv3330.1	3	1uwj_BAX_B_1723 PDB CREDO	0.527	0.277	0.527	0.007
Rv3330.1	3	1hwi_115_B_1 PDB CREDO	0.595	0.185	0.527	0.007
Rv3330.1	6	1gwr_EST_B_600 PDB CREDO	0.526	0.278	0.526	0.007
Rv3330.1	3	1hwi_115_D_3 PDB CREDO	0.595	0.185	0.526	0.007
Rv3330.1	3	3tne_RIT_B_401 PDB CREDO	0.595	0.185	0.526	0.007
Rv3330.1	6	1pbc_BHA_A_396 PDB CREDO	0.551	0.243	0.526	0.007
Rv3330.1	3	1uwj_BAX_A_1723 PDB CREDO	0.574	0.212	0.526	0.007
Rv3330.1	6	3nt1_NPS_A_5 PDB CREDO	0.681	0.096	0.526	0.007
Rv3330.1	6	3nt1_NPS_B_4 PDB CREDO	0.681	0.096	0.526	0.007
Rv3330.1	6	1g50_EST_B_1600 PDB CREDO	0.525	0.280	0.525	0.007
Rv3330.1	6	1qku_EST_A_600 PDB CREDO	0.524	0.281	0.524	0.008
Rv3330.1	6	1qku_EST_B_600 PDB CREDO	0.524	0.281	0.524	0.008
Rv3330.1	6	2jj8_AZZ_D_1211 PDB CREDO	0.549	0.245	0.524	0.008
Rv3330.1	6	1pcg_EST_B_2 PDB CREDO	0.523	0.283	0.523	0.008
Rv3330.3	3	1hwl_FBI_C_4 PDB CREDO	0.555	0.237	0.522	0.008
Rv3330.3	3	1hwl_FBI_D_3 PDB CREDO	0.555	0.237	0.522	0.008
Rv3330.1	6	1qku_EST_C_600 PDB CREDO	0.522	0.284	0.522	0.008
Rv3330.1	6	2jj8_AZZ_C_1211 PDB CREDO	0.547	0.248	0.522	0.008
Rv3330.3	3	1hwl_FBI_B_1 PDB CREDO	0.554	0.238	0.521	0.008
Rv3330.1	6	1cqp_803_A_311 PDB CREDO	0.521	0.286	0.521	0.008
Rv3330.1	6	2jj8_AZZ_B_1211 PDB CREDO	0.546	0.250	0.521	0.008
Rv3330.3	3	1hwl_FBI_A_2 PDB CREDO	0.553	0.239	0.521	0.008
Rv3330.3	3	1hwk_117_C_4 PDB CREDO	0.569	0.218	0.520	0.008
Rv3330.3	3	1hwk_117_A_2 PDB CREDO	0.569	0.218	0.519	0.008
Rv3330.1	6	2jj8_AZZ_A_1211 PDB CREDO	0.544	0.253	0.519	0.008
Rv3330.1	6	1lw0_NVP_A_999 PDB CREDO	0.699	0.082	0.518	0.008
Rv3330.1	6	3n8z_FLP_B_1701 PDB CREDO	0.671	0.105	0.518	0.008
Rv3330.1	6	1s9p_DES_B_459 PDB CREDO	0.697	0.083	0.517	0.008
Rv3330.1	6	1s9p_DES_C_500 PDB CREDO	0.697	0.083	0.517	0.008
Rv3330.1	3	3tkd_CYZ_B_267 PDB CREDO	0.547	0.248	0.515	0.009
Rv3330.1	6	2bxq_IMN_A_2001 PDB CREDO	0.624	0.151	0.515	0.009
Rv3330.1	6	2bxg_IBP_B_2001 PDB CREDO	0.588	0.194	0.514	0.009
Rv3330.1	6	2ayl_FLP_B_2701 PDB CREDO	0.638	0.136	0.514	0.009
Rv3330.1	3	3tne_RIT_A_401 PDB CREDO	0.580	0.204	0.513	0.009
Rv3330.3	3	1hwi_115_B_1 PDB CREDO	0.529	0.275	0.512	0.009
Rv3330.1	6	1fk9_EFZ_A_999 PDB CREDO	0.689	0.089	0.511	0.009
Rv3330.1	3	3tkd_CYZ_A_266 PDB CREDO	0.577	0.207	0.511	0.009
Rv3330.3	3	1hwi_115_D_3 PDB CREDO	0.527	0.277	0.511	0.009
Rv3330.1	6	2efj_37T_A_502 PDB CREDO	0.535	0.266	0.511	0.009
Rv3330.1	6	3rf4_FUN_A_201 PDB CREDO	0.619	0.157	0.511	0.009
Rv3330.1	6	3rf4_FUN_C_203 PDB CREDO	0.618	0.158	0.510	0.009
Rv3330.1	6	4enh_FVX_A_602 PDB CREDO	0.533	0.269	0.509	0.009
Rv3330.1	3	1uwh_BAX_B_1723 PDB CREDO	0.539	0.260	0.507	0.010
Rv3330.1	6	3rf4_FUN_B_202 PDB CREDO	0.615	0.161	0.507	0.010
Rv3330.1	3	1uwh_BAX_A_1723 PDB CREDO	0.538	0.261	0.507	0.010
Rv3330.1	6	3hgx_SAL_A_102 PDB CREDO	0.719	0.067	0.506	0.010
Rv3330.1	3	1hwi_115_A_2 PDB CREDO	0.628	0.147	0.504	0.010
Rv3330.1	6	3ret_SAL_A_201 PDB CREDO	0.716	0.069	0.504	0.010
Rv3330.1	6	3mdv_CL6_A_506 PDB CREDO	0.503	0.313	0.503	0.010
Rv3330.1	3	3frq_ERY_A_195 PDB CREDO	0.518	0.291	0.503	0.010
Rv3330.1	6	1pxx_DIF_A_701 PDB CREDO	0.574	0.212	0.502	0.011
Rv3330.1	6	3hgx_SAL_B_104 PDB CREDO	0.713	0.071	0.502	0.011
Rv3330.1	6	2bxf_DZP_B_2001 PDB CREDO	0.501	0.317	0.501	0.011
Rv3330.3	3	3n58_ADN_A_500 PDB CREDO	0.653	0.122	0.501	0.011

Similarity to known drug target from sensitive sequence analysis

DrugBank ID	Drug Name
DB00274DrugBank	Cefmetazole
DB00303DrugBank	Ertapenem
DB00319DrugBank	Piperacillin
DB00415DrugBank	Ampicillin
DB00430DrugBank	Cefpiramide
DB00438DrugBank	Ceftazidime
DB00447DrugBank	Loracarbef
DB00456DrugBank	Cefalotin
DB00485DrugBank	Dicloxacillin
DB00567DrugBank	Cephalexin
DB00607DrugBank	Nafcillin
DB00713DrugBank	Oxacillin
DB00739DrugBank	Hetacillin
DB00833DrugBank	Cefaclor
DB00948DrugBank	Mezlocillin
DB01000DrugBank	Cyclacillin
DB01140DrugBank	Cefadroxil
DB01147DrugBank	Cloxacillin
DB01163DrugBank	Amdinocillin
DB01329DrugBank	Cefoperazone
DB01330DrugBank	Cefotetan
DB01331DrugBank	Cefoxitin
DB01603DrugBank	Meticillin
DB08795DrugBank	Azidocillin

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
lipid intermediate IIPubChem	0.9	1920.24
C05898PubChem	0.9	1920.24