SInCRe - Rv2996c

Tuberculist information

Gene name	serA1
Protein function	Probable D-3-phosphoglycerate dehydrogenase SerA1 (PGDH)
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	3353.48
Molecular mass(da)	54522.2
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 528

	  		  	1    VSLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVL   60
			  	61   AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAA  120
			  	121  DASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAA  180
			  	181  QLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAA  240
			  	241  LADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVR  300
			  	301  LALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEE  360
			  	361  VEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGAD  420
			  	421  GSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVN  480
			  	481  IQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS

Known structures in the PDB

	PDB ID	1YGY
	Total residue count	1058
	Number of chains	2
	Method	X-RAY
	Resolution	2.3

	PDB ID	3DC2
	Total residue count	1058
	Number of chains	2
	Method	X-RAY
	Resolution	2.7

	PDB ID	3DDN
	Total residue count	1056
	Number of chains	2
	Method	X-RAY
	Resolution	2.4

Number of amino acids : 528

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
2-Hacid_dh	PF00389	6-313
2-Hacid_dh_C	PF02826	107-281
ACT	PF01842	454-518

Mtb Structural Proteome models

Model Number	1
Model name	Rv2996c_1ygy_A
Template	1YGY APDB CREDO
Template coverage	3_529
Template Identity(%)	100.0
Model coverage(%)	99.6
Normalized DOPE score	-1.025

Model Number	2
Model name	Rv2996c
Template	1YGY APDB CREDO
Template coverage	3_529
Template Identity(%)	100.0
Model coverage(%)	99.6
Normalized DOPE score	-0.837

Structure Models from Chopin

Model Number	1
Profile	c.2.1.4, d.58.18.1, d.81.2.2 - 3.30.1330.90, 3.40.50.720 Click for model details
zscore	90.29
Residue begin	2
Residue end	528

Model Number	2
Profile	c.2.1.4 Click for model details
zscore	27.19
Residue begin	107
Residue end	281

Model Number	3
Profile	d.81.2.2 Click for model details
zscore	26.27
Residue begin	316
Residue end	450

Model Number	4
Profile	c.2.1.4 Click for model details
zscore	16.79
Residue begin	94
Residue end	327

Model Number	5
Profile	d.58.18.1 Click for model details
zscore	16.28
Residue begin	444
Residue end	528

Binding pockets

STRING

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

Protein interacting with Rv2996c	Gene name	Confidence Score
Rv0884c	serC	0.998
Rv3042c	serB2	0.988
Rv3042c	serB2	0.988
Rv1617	pykA	0.98
Rv1617	pykA	0.98
Rv0489	gpm1	0.939
Rv2205c	Rv2205c	0.924
Rv2995c	leuB	0.919
Rv3709c	ask	0.907
Rv3709c	ask	0.907
Rv3709c	ask	0.907
Rv3838c	pheA	0.904
Rv3838c	pheA	0.904
Rv2419c	Rv2419c	0.901

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv2996c_1ygy_A	19	3pww_ROC_A_1001 PDB CREDO	0.654	0.120	0.654	0.001
Rv2996c_1ygy_A	19	1c6y_MK1_B_524 PDB CREDO	0.654	0.120	0.637	0.001
Rv2996c_1ygy_A	19	1t46_STI_A_3 PDB CREDO	0.634	0.141	0.634	0.001
Rv2996c_1ygy_A	19	2fxd_DR7_A_102 PDB CREDO	0.625	0.151	0.608	0.002
Rv2996c_1ygy_A	19	3prs_RIT_A_1001 PDB CREDO	0.706	0.076	0.606	0.002
Rv2996c_1ygy_A	19	3el9_DR7_A_100 PDB CREDO	0.619	0.157	0.603	0.002
Rv2996c_1ygy_A	19	1c6z_ROC_B_505 PDB CREDO	0.671	0.105	0.590	0.003
Rv2996c_1ygy_A	19	3ufn_ROC_A_401 PDB CREDO	0.604	0.175	0.588	0.003
Rv2996c_1ygy_A	19	1n49_RIT_B_301 PDB CREDO	0.634	0.141	0.585	0.003
Rv2996c_1ygy_A	19	3ekq_ROC_A_100 PDB CREDO	0.617	0.159	0.585	0.003
Rv2996c_1ygy_A	19	3cs9_NIL_C_600 PDB CREDO	0.578	0.206	0.578	0.003
Rv2996c_1ygy_A	19	3cs9_NIL_D_600 PDB CREDO	0.576	0.209	0.576	0.003
Rv2996c_1ygy_A	19	3s56_ROC_A_201 PDB CREDO	0.580	0.204	0.565	0.004
Rv2996c_1ygy_A	4	3oxc_ROC_A_401 PDB CREDO	0.575	0.211	0.562	0.004
Rv2996c_1ygy_A	19	3gp0_NIL_A_1 PDB CREDO	0.576	0.208	0.562	0.004
Rv2996c_1ygy_A	19	1opj_STI_A_3 PDB CREDO	0.604	0.175	0.556	0.004
Rv2996c_1ygy_A	19	2qxs_RAL_B_600 PDB CREDO	0.586	0.196	0.556	0.005
Rv2996c_1ygy_A	19	2qxs_RAL_A_600 PDB CREDO	0.584	0.198	0.554	0.005
Rv2996c_1ygy_A	19	1opj_STI_B_4 PDB CREDO	0.598	0.181	0.552	0.005
Rv2996c_1ygy_A	4	1xkk_FMM_A_91 PDB CREDO	0.801	0.024	0.550	0.005
Rv2996c_1ygy_A	19	3k5v_STI_A_2 PDB CREDO	0.613	0.163	0.550	0.005
Rv2996c_1ygy_A	19	3q70_RIT_A_2001 PDB CREDO	0.708	0.075	0.549	0.005
Rv2996c_1ygy_A	4	2q64_1UN_B_1001 PDB CREDO	0.740	0.054	0.548	0.005
Rv2996c_1ygy_A	19	1t7j_478_A_200 PDB CREDO	0.728	0.061	0.548	0.005
Rv2996c_1ygy_A	4	2qak_1UN_A_1001 PDB CREDO	0.738	0.055	0.547	0.005
Rv2996c_1ygy_A	4	2pym_1UN_A_1001 PDB CREDO	0.736	0.056	0.546	0.005
Rv2996c_1ygy_A	19	3rgf_BAX_A_465 PDB CREDO	0.626	0.150	0.546	0.005
Rv2996c_1ygy_A	4	2pyn_1UN_A_1001 PDB CREDO	0.735	0.057	0.545	0.005
Rv2996c_1ygy_A	4	2q63_1UN_A_1001 PDB CREDO	0.734	0.057	0.544	0.006
Rv2996c_1ygy_A	19	1n49_RIT_D_401 PDB CREDO	0.641	0.133	0.543	0.006
Rv2996c_1ygy_A	19	3lzv_017_A_200 PDB CREDO	0.606	0.172	0.543	0.006
Rv2996c_1ygy_A	19	3el0_1UN_A_201 PDB CREDO	0.604	0.174	0.542	0.006
Rv2996c_1ygy_A	19	4asd_BAX_A_1500 PDB CREDO	0.678	0.098	0.542	0.006
Rv2996c_1ygy_A	19	3so9_017_A_100 PDB CREDO	0.719	0.067	0.541	0.006
Rv2996c_1ygy_A	4	3sm2_478_A_126 PDB CREDO	0.748	0.049	0.541	0.006
Rv2996c_1ygy_A	19	1sh9_RIT_B_301 PDB CREDO	0.556	0.236	0.541	0.006
Rv2996c_1ygy_A	19	3oez_STI_A_601 PDB CREDO	0.638	0.136	0.541	0.006
Rv2996c_1ygy_A	19	3el4_ROC_A_100 PDB CREDO	0.676	0.100	0.540	0.006
Rv2996c_1ygy_A	19	1hsh_MK1_A_401 PDB CREDO	0.554	0.238	0.540	0.006
Rv2996c_1ygy_A	19	1xkk_FMM_A_91 PDB CREDO	0.568	0.219	0.539	0.006
Rv2996c_1ygy_A	4	3k4v_ROC_B_201 PDB CREDO	0.560	0.230	0.537	0.006
Rv2996c_1ygy_A	4	3gp0_NIL_A_1 PDB CREDO	0.802	0.024	0.537	0.006
Rv2996c_1ygy_A	19	1ohr_1UN_A_201 PDB CREDO	0.551	0.242	0.537	0.006
Rv2996c_1ygy_A	19	3ogq_AB1_A_200 PDB CREDO	0.580	0.204	0.537	0.006
Rv2996c_1ygy_A	19	2q64_1UN_B_1001 PDB CREDO	0.609	0.169	0.535	0.006
Rv2996c_1ygy_A	4	3ucb_017_A_201 PDB CREDO	0.671	0.105	0.535	0.006
Rv2996c_1ygy_A	19	2hyy_STI_C_600 PDB CREDO	0.631	0.144	0.534	0.006
Rv2996c_1ygy_A	19	1hsh_MK1_C_402 PDB CREDO	0.548	0.246	0.534	0.006
Rv2996c_1ygy_A	19	2pym_1UN_A_1001 PDB CREDO	0.607	0.171	0.534	0.006
Rv2996c_1ygy_A	19	2qak_1UN_A_1001 PDB CREDO	0.607	0.171	0.534	0.006
Rv2996c_1ygy_A	19	2hyy_STI_A_600 PDB CREDO	0.630	0.145	0.534	0.007
Rv2996c_1ygy_A	19	3k5v_STI_B_2 PDB CREDO	0.630	0.145	0.534	0.007
Rv2996c_1ygy_A	19	2q63_1UN_A_1001 PDB CREDO	0.606	0.171	0.533	0.007
Rv2996c_1ygy_A	19	3mss_STI_C_1 PDB CREDO	0.629	0.146	0.533	0.007
Rv2996c_1ygy_A	19	2pyn_1UN_A_1001 PDB CREDO	0.606	0.172	0.533	0.007
Rv2996c_1ygy_A	19	2hyy_STI_D_600 PDB CREDO	0.629	0.146	0.533	0.007
Rv2996c_1ygy_A	19	3gvu_STI_A_1001 PDB CREDO	0.628	0.147	0.532	0.007
Rv2996c_1ygy_A	19	3ms9_STI_A_1 PDB CREDO	0.628	0.147	0.532	0.007
Rv2996c_1ygy_A	19	3mss_STI_D_1 PDB CREDO	0.628	0.147	0.532	0.007
Rv2996c_1ygy_A	19	3mss_STI_A_1 PDB CREDO	0.627	0.148	0.531	0.007
Rv2996c_1ygy_A	19	3pyy_STI_B_4 PDB CREDO	0.627	0.149	0.531	0.007
Rv2996c_1ygy_A	19	1rl8_RIT_A_9001 PDB CREDO	0.618	0.158	0.531	0.007
Rv2996c_1ygy_A	19	3mss_STI_B_1 PDB CREDO	0.626	0.149	0.531	0.007
Rv2996c_1ygy_A	19	3sm2_478_A_126 PDB CREDO	0.588	0.194	0.530	0.007
Rv2996c_1ygy_A	19	3ms9_STI_B_1 PDB CREDO	0.626	0.150	0.530	0.007
Rv2996c_1ygy_A	19	1iep_STI_B_202 PDB CREDO	0.624	0.151	0.529	0.007
Rv2996c_1ygy_A	19	3ggu_017_B_201 PDB CREDO	0.557	0.234	0.529	0.007
Rv2996c_1ygy_A	4	3ndt_ROC_A_101 PDB CREDO	0.563	0.226	0.529	0.007
Rv2996c_1ygy_A	19	1iep_STI_A_201 PDB CREDO	0.624	0.151	0.529	0.007
Rv2996c_1ygy_A	19	3pyy_STI_A_3 PDB CREDO	0.623	0.153	0.528	0.007
Rv2996c_1ygy_A	19	3ndt_ROC_D_100 PDB CREDO	0.644	0.131	0.526	0.007
Rv2996c_1ygy_A	19	1uwj_BAX_A_1723 PDB CREDO	0.604	0.175	0.526	0.007
Rv2996c_1ygy_A	19	2nnk_ROC_A_401 PDB CREDO	0.642	0.132	0.525	0.007
Rv2996c_1ygy_A	4	3tkg_ROC_B_801 PDB CREDO	0.535	0.265	0.524	0.008
Rv2996c_1ygy_A	19	2f80_017_B_301 PDB CREDO	0.595	0.185	0.523	0.008
Rv2996c_1ygy_A	19	2pl0_STI_A_200 PDB CREDO	0.674	0.102	0.523	0.008
Rv2996c_1ygy_A	4	1k6c_MK1_B_902 PDB CREDO	0.638	0.137	0.521	0.008
Rv2996c_1ygy_A	4	3ndu_ROC_D_100 PDB CREDO	0.594	0.187	0.520	0.008
Rv2996c_1ygy_A	4	3d1x_ROC_A_201 PDB CREDO	0.530	0.272	0.519	0.008
Rv2996c_1ygy_A	19	3cs9_NIL_A_600 PDB CREDO	0.562	0.227	0.519	0.008
Rv2996c_1ygy_A	4	3el4_ROC_A_100 PDB CREDO	0.634	0.141	0.518	0.008
Rv2996c_1ygy_A	4	1t7i_017_A_200 PDB CREDO	0.634	0.141	0.518	0.008
Rv2996c_1ygy_A	4	2nmy_ROC_A_401 PDB CREDO	0.578	0.207	0.518	0.008
Rv2996c_1ygy_A	4	3k4v_ROC_D_201 PDB CREDO	0.616	0.160	0.515	0.009
Rv2996c_1ygy_A	19	3el5_1UN_B_201 PDB CREDO	0.571	0.216	0.515	0.009
Rv2996c_1ygy_A	19	1hxw_RIT_B_301 PDB CREDO	0.542	0.255	0.515	0.009
Rv2996c_1ygy_A	19	3cs9_NIL_B_600 PDB CREDO	0.543	0.254	0.515	0.009
Rv2996c_1ygy_A	19	2hyy_STI_B_600 PDB CREDO	0.663	0.112	0.514	0.009
Rv2996c_1ygy_A	19	1hxb_ROC_A_100 PDB CREDO	0.584	0.198	0.514	0.009
Rv2996c_1ygy_A	19	3spk_TPV_B_100 PDB CREDO	0.624	0.152	0.513	0.009
Rv2996c_1ygy_A	4	3cyx_ROC_A_201 PDB CREDO	0.586	0.197	0.513	0.009
Rv2996c_1ygy_A	4	1rl8_RIT_A_9001 PDB CREDO	0.674	0.102	0.512	0.009
Rv2996c_1ygy_A	4	3tl9_ROC_A_401 PDB CREDO	0.545	0.251	0.511	0.009
Rv2996c_1ygy_A	4	3ndt_ROC_D_100 PDB CREDO	0.640	0.134	0.511	0.009
Rv2996c_1ygy_A	4	2nnk_ROC_A_401 PDB CREDO	0.639	0.136	0.509	0.009
Rv2996c_1ygy_A	19	1uwh_BAX_B_1723 PDB CREDO	0.676	0.100	0.509	0.009
Rv2996c_1ygy_A	19	1uwh_BAX_A_1723 PDB CREDO	0.676	0.100	0.509	0.010
Rv2996c_1ygy_A	4	1c6z_ROC_B_505 PDB CREDO	0.685	0.093	0.508	0.010
Rv2996c_1ygy_A	19	1sgu_MK1_B_2632 PDB CREDO	0.597	0.183	0.506	0.010
Rv2996c_1ygy_A	4	1t46_STI_A_3 PDB CREDO	0.774	0.035	0.505	0.010
Rv2996c_1ygy_A	19	1k6c_MK1_B_902 PDB CREDO	0.632	0.143	0.504	0.010
Rv2996c_1ygy_A	19	3k4v_ROC_D_201 PDB CREDO	0.644	0.130	0.502	0.011
Rv2996c_1ygy_A	1	2y7j_B49_D_1294 PDB CREDO	0.572	0.215	0.502	0.011
Rv2996c_1ygy_A	19	2v0z_C41_O_1327 PDB CREDO	0.515	0.296	0.501	0.011
Rv2996c_1ygy_A	19	2r5q_1UN_D_900 PDB CREDO	0.608	0.170	0.500	0.011
Rv2996c_1ygy_A	19	3ogp_017_B_200 PDB CREDO	0.590	0.191	0.500	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
phosphohydroxypyruvatePubChem	0.995	184.041
NAD+PubChem	0.985	663.425
tartratePubChem	0.979	150.087
L-serinePubChem	0.959	105.093
3-phosphoglyceratePubChem	0.95	186.057
alpha-ketoglutaratePubChem	0.947	146.098
O-phosphoserinePubChem	0.933	185.072
glutamatePubChem	0.931	147.129
reduced nicotinamide adenine dinucleotidePubChem	0.929	665.441
lactatePubChem	0.92	90.0779
D-lactatePubChem	0.913	90.0779
H(+)PubChem	0.906	2.01588
deuteriumPubChem	0.906	2.01588
L-alaninePubChem	0.906	89.0932
adenosine diphosphatePubChem	0.903	427.201
phosphoenolpyruvatePubChem	0.901	168.042
propionyl-CoAPubChem	0.9	823.597
n-propionyl-CoAPubChem	0.9	823.597
lactyl-CoAPubChem	0.9	839.597
L-tartratePubChem	0.9	148.071
adenosine triphosphatePubChem	0.9	507.181
d-tartratePubChem	0.9	150.087
propionatePubChem	0.9	74.0785
D-lactoyl-CoAPubChem	0.9	835.565
dihydronicotinamide formycin dinucleotidePubChem	0.9	665.441
pyruvic acidPubChem	0.9	88.0621
protiumPubChem	0.9	2.01576
meso-tartratePubChem	0.8	148.071