SInCRe - Rv1201c

Tuberculist information

Gene name	dapD
Protein function	Tetrahydrodipicolinate N-succinyltransferase DapD
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	1344.22
Molecular mass(da)	32609.8
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 317

	  		  	1    VSTVTGAAGIGLATLAADGSVLDTWFPAPELTESGTSATSRLAVSDVPVELAALIGRDDD   60
			  	61   RRTETIAVRTVIGSLDDVAADPYDAYLRLHLLSHRLVAPHGLNAGGLFGVLTNVVWTNHG  120
			  	121  PCAIDGFEAVRARLRRRGPVTVYGVDKFPRMVDYVVPTGVRIADADRVRLGAHLAPGTTV  180
			  	181  MHEGFVNYNAGTLGASMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTHVISIGKRCLL  240
			  	241  GANSGLGISLGDDCVVEAGLYVTAGTRVTMPDSNSVKARELSGSSNLLFRRNSVSGAVEV  300
			  	301  LARDGQGIALNEDLHAN

Known structures in the PDB

	PDB ID	3FSX
	Total residue count	1660
	Number of chains	5
	Method	X-RAY
	Resolution	2.15

	PDB ID	3FSY
	Total residue count	1660
	Number of chains	5
	Method	X-RAY
	Resolution	1.97

Number of amino acids : 317

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
THDPS_M	PF14789	111-150
Hexapep_2	PF14602	231-264

Mtb Structural Proteome models

Model Number	1
Model name	Rv1201c_3fsy_A
Template	3FSY APDB CREDO
Template coverage	4_310
Template Identity(%)	100.0
Model coverage(%)	96.5
Normalized DOPE score	-1.059

Model Number	2
Model name	Rv1201c
Template	1QRE APDB CREDO
Template coverage	5_173
Template Identity(%)	21.7
Model coverage(%)	43.2
Normalized DOPE score	0.15

Structure Models from Chopin

Model Number	1
Profile	3.30.60.70 Click for model details
zscore	13.73
Residue begin	111
Residue end	150

Model Number	2
Profile	b.81.1.2 Click for model details
zscore	10.73
Residue begin	13
Residue end	317

Binding pockets

STRING

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

Protein interacting with Rv1201c	Gene name	Confidence Score
Rv2773c	dapB	0.969
Rv2773c	dapB	0.969

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv1201c_3fsy_A	2	1uwj_BAX_B_1723 PDB CREDO	0.581	0.203	0.564	0.004
Rv1201c_3fsy_A	12	1uwj_BAX_B_1723 PDB CREDO	0.608	0.169	0.555	0.005
Rv1201c_3fsy_A	2	1uwj_BAX_A_1723 PDB CREDO	0.621	0.155	0.552	0.005
Rv1201c_3fsy_A	12	1uwh_BAX_B_1723 PDB CREDO	0.568	0.220	0.551	0.005
Rv1201c_3fsy_A	12	1uwh_BAX_A_1723 PDB CREDO	0.567	0.221	0.550	0.005
Rv1201c_3fsy_A	2	1uwh_BAX_A_1723 PDB CREDO	0.561	0.228	0.545	0.005
Rv1201c_3fsy_A	2	1uwh_BAX_B_1723 PDB CREDO	0.561	0.228	0.545	0.005
Rv1201c_3fsy_A	12	3ua1_08Y_A_600 PDB CREDO	0.577	0.208	0.542	0.006
Rv1201c_3fsy_A	2	3d91_REM_A_350 PDB CREDO	0.554	0.239	0.537	0.006
Rv1201c_3fsy_A	2	3d91_REM_B_350 PDB CREDO	0.553	0.240	0.536	0.006
Rv1201c_3fsy_A	12	1uob_PNN_A_1311 PDB CREDO	0.568	0.219	0.535	0.006
Rv1201c_3fsy_A	12	1uwj_BAX_A_1723 PDB CREDO	0.635	0.140	0.532	0.007
Rv1201c_3fsy_A	12	1fm6_BRL_X_504 PDB CREDO	0.563	0.226	0.528	0.007
Rv1201c_3fsy_A	12	3vn2_TLS_A_501 PDB CREDO	0.527	0.277	0.527	0.007
Rv1201c_3fsy_A	2	3tne_RIT_A_401 PDB CREDO	0.575	0.210	0.525	0.007
Rv1201c_3fsy_A	12	1y0x_T44_X_500 PDB CREDO	0.541	0.257	0.524	0.008
Rv1201c_3fsy_A	2	3tne_RIT_B_401 PDB CREDO	0.572	0.214	0.522	0.008
Rv1201c_3fsy_A	2	1uob_PNN_A_1311 PDB CREDO	0.519	0.289	0.519	0.008
Rv1201c_3fsy_A	12	2x9g_LYA_A_1270 PDB CREDO	0.552	0.241	0.518	0.008
Rv1201c_3fsy_A	2	1z2b_VLB_C_800 PDB CREDO	0.517	0.293	0.517	0.008
Rv1201c_3fsy_A	12	2hyy_STI_B_600 PDB CREDO	0.547	0.249	0.514	0.009
Rv1201c_3fsy_A	12	3ln1_CEL_C_682 PDB CREDO	0.564	0.224	0.513	0.009
Rv1201c_3fsy_A	12	3ln1_CEL_B_682 PDB CREDO	0.564	0.225	0.512	0.009
Rv1201c_3fsy_A	12	3ln1_CEL_A_682 PDB CREDO	0.563	0.226	0.512	0.009
Rv1201c_3fsy_A	12	2oiq_STI_A_1001 PDB CREDO	0.544	0.253	0.512	0.009
Rv1201c_3fsy_A	12	1xzx_T3_X_500 PDB CREDO	0.544	0.253	0.511	0.009
Rv1201c_3fsy_A	12	3uvv_T3_A_501 PDB CREDO	0.542	0.256	0.509	0.010
Rv1201c_3fsy_A	12	2hw2_RFP_A_1200 PDB CREDO	0.523	0.283	0.507	0.010
Rv1201c_3fsy_A	12	3gws_T3_X_500 PDB CREDO	0.557	0.234	0.506	0.010
Rv1201c_3fsy_A	12	3nxu_RIT_A_600 PDB CREDO	0.655	0.120	0.504	0.010
Rv1201c_3fsy_A	2	3tkd_CYZ_B_267 PDB CREDO	0.519	0.289	0.504	0.010
Rv1201c_3fsy_A	12	2hyy_STI_A_600 PDB CREDO	0.583	0.200	0.502	0.011
Rv1201c_3fsy_A	12	4asd_BAX_A_1500 PDB CREDO	0.550	0.245	0.502	0.011
Rv1201c_3fsy_A	12	3b0w_DGX_B_1 PDB CREDO	0.616	0.160	0.502	0.011
Rv1201c_3fsy_A	12	3nxu_RIT_B_600 PDB CREDO	0.651	0.123	0.501	0.011
Rv1201c_3fsy_A	12	3mss_STI_D_1 PDB CREDO	0.582	0.202	0.501	0.011
Rv1201c_3fsy_A	12	3oez_STI_B_601 PDB CREDO	0.517	0.292	0.501	0.011
Rv1201c_3fsy_A	12	3b0w_DGX_A_1 PDB CREDO	0.549	0.246	0.501	0.011
Rv1201c_3fsy_A	12	2hyy_STI_C_600 PDB CREDO	0.581	0.202	0.501	0.011
Rv1201c_3fsy_A	12	3gvu_STI_A_1001 PDB CREDO	0.581	0.202	0.501	0.011
Rv1201c_3fsy_A	12	3ms9_STI_B_1 PDB CREDO	0.581	0.202	0.501	0.011
Rv1201c_3fsy_A	12	3pyy_STI_A_3 PDB CREDO	0.581	0.202	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
L-2,3,4,5-tetrahydrodipicolinatePubChem	0.949	171.151
delta1-piperideine-2,6-dicarboxylatePubChem	0.948	171.151
succinyl-CoAPubChem	0.94	867.607
2-methyl-2,4-pentanediolPubChem	0.9	118.174
hydride acetatePubChem	0.9	61.0599
magnesiumPubChem	0.9	24.305
succinyl-coenzyme APubChem	0.9	867.607
(4s)-2-Methyl-2,4-PentanediolPubChem	0.9	118.174
acetatePubChem	0.9	59.044
Na(+)PubChem	0.9	22.9898
citratePubChem	0.713	192.124