SInCRe - Rv3423c

Tuberculist information

Gene name	alr
Protein function	Alanine racemase Alr
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	3840.19
Molecular mass(da)	43355.6
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 408

	  		  	1    VKRFWENVGKPNDTTDGRGTTSLAMTPISQTPGLLAEAMVDLGAIEHNVRVLREHAGHAQ   60
			  	61   LMAVVKADGYGHGATRVAQTALGAGAAELGVATVDEALALRADGITAPVLAWLHPPGIDF  120
			  	121  GPALLADVQVAVSSLRQLDELLHAVRRTGRTATVTVKVDTGLNRNGVGPAQFPAMLTALR  180
			  	181  QAMAEDAVRLRGLMSHMVYADKPDDSINDVQAQRFTAFLAQAREQGVRFEVAHLSNSSAT  240
			  	241  MARPDLTFDLVRPGIAVYGLSPVPALGDMGLVPAMTVKCAVALVKSIRAGEGVSYGHTWI  300
			  	301  APRDTNLALLPIGYADGVFRSLGGRLEVLINGRRCPGVGRICMDQFMVDLGPGPLDVAEG  360
			  	361  DEAILFGPGIRGEPTAQDWADLVGTIHYEVVTSPRGRITRTYREAENR

Known structures in the PDB

	PDB ID	1XFC
	Total residue count	768
	Number of chains	2
	Method	X-RAY
	Resolution	1.9

Number of amino acids : 408

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
Ala_racemase_N	PF01168	40-262
Ala_racemase_C	PF00842	274-403

Mtb Structural Proteome models

Model Number	1
Model name	Rv3423c_1xfc_A
Template	1XFC APDB CREDO
Template coverage	11_381
Template Identity(%)	100.0
Model coverage(%)	90.7
Normalized DOPE score	-1.444

Model Number	2
Model name	Rv3423c
Template	1XFC APDB CREDO
Template coverage	11_381
Template Identity(%)	98.6
Model coverage(%)	90.7
Normalized DOPE score	-1.025

Model Number	3
Model name	Rv3423c.1
Template	1HKV APDB CREDO
Template coverage	2_428
Template Identity(%)	19.0
Model coverage(%)	99.3
Normalized DOPE score	0.522

Structure Models from Chopin

Model Number	1
Profile	2.40.37.10, 3.20.20.10 Click for model details
zscore	48.14
Residue begin	1
Residue end	408

Model Number	2
Profile	c.1.6.1 Click for model details
zscore	30.99
Residue begin	40
Residue end	262

Model Number	3
Profile	2.40.37.10 Click for model details
zscore	24.32
Residue begin	274
Residue end	403

Model Number	4
Profile	c.1.6.1 Click for model details
zscore	24.11
Residue begin	33
Residue end	408

Model Number	5
Profile	2.40.37.10 Click for model details
zscore	17.46
Residue begin	204
Residue end	408

Binding pockets

STRING

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

Protein interacting with Rv3423c	Gene name	Confidence Score
Rv2981c	ddlA	0.998
Rv2981c	ddlA	0.998
Rv2780	ald	0.996
Rv2780	ald	0.996
Rv3422c	Rv3422c	0.986
Rv2157c	murF	0.979
Rv2157c	murF	0.979
Rv2157c	murF	0.979
Rv3420c	rimI	0.973
Rv3421c	Rv3421c	0.942
Rv3419c	gcp	0.941
Rv0337c	aspC	0.94
Rv1293	lysA	0.92
Rv1293	lysA	0.92

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv3423c.1	9	3ug2_IRE_A_1 PDB CREDO	0.712	0.072	0.677	0.000
Rv3423c.1	9	1xbb_STI_A_1 PDB CREDO	0.692	0.087	0.659	0.001
Rv3423c.1	18	1xkk_FMM_A_91 PDB CREDO	0.775	0.035	0.637	0.001
Rv3423c.1	18	3gp0_NIL_A_1 PDB CREDO	0.755	0.045	0.604	0.002
Rv3423c.1	18	2xkw_P1B_A_1478 PDB CREDO	0.702	0.079	0.592	0.002
Rv3423c.1	9	3r9c_ECL_A_451 PDB CREDO	0.617	0.160	0.586	0.003
Rv3423c.1	18	1t46_STI_A_3 PDB CREDO	0.743	0.052	0.579	0.003
Rv3423c.1	9	3jw5_TOP_B_208 PDB CREDO	0.607	0.170	0.577	0.003
Rv3423c.1	9	2nnj_225_A_501 PDB CREDO	0.596	0.184	0.567	0.004
Rv3423c.1	18	3sm2_478_A_126 PDB CREDO	0.651	0.124	0.563	0.004
Rv3423c.1	9	3jw5_TOP_A_208 PDB CREDO	0.588	0.193	0.559	0.004
Rv3423c.1	18	1c6z_ROC_B_505 PDB CREDO	0.628	0.147	0.557	0.004
Rv3423c.1	9	3vkx_T3_A_301 PDB CREDO	0.612	0.165	0.554	0.005
Rv3423c.1	9	3ads_IMN_B_3 PDB CREDO	0.760	0.042	0.549	0.005
Rv3423c.1	18	3k4v_ROC_D_201 PDB CREDO	0.546	0.250	0.546	0.005
Rv3423c.1	18	3ucb_017_A_201 PDB CREDO	0.571	0.215	0.545	0.005
Rv3423c.1	18	1k6c_MK1_B_902 PDB CREDO	0.557	0.234	0.544	0.005
Rv3423c.1	18	2nnk_ROC_A_401 PDB CREDO	0.569	0.219	0.542	0.006
Rv3423c.1	18	3ndt_ROC_D_100 PDB CREDO	0.568	0.219	0.542	0.006
Rv3423c.1	18	3el4_ROC_A_100 PDB CREDO	0.555	0.238	0.542	0.006
Rv3423c.1	18	3cs9_NIL_D_600 PDB CREDO	0.694	0.085	0.541	0.006
Rv3423c.1	18	2qak_1UN_A_1001 PDB CREDO	0.608	0.169	0.539	0.006
Rv3423c.1	18	3cs9_NIL_C_600 PDB CREDO	0.692	0.087	0.539	0.006
Rv3423c.1	9	1uay_ADN_A_1001 PDB CREDO	0.654	0.121	0.539	0.006
Rv3423c.1	18	2q64_1UN_B_1001 PDB CREDO	0.606	0.172	0.537	0.006
Rv3423c.1	9	3uq6_ADN_A_401 PDB CREDO	0.621	0.155	0.536	0.006
Rv3423c.1	9	3uq6_ADN_B_401 PDB CREDO	0.621	0.155	0.536	0.006
Rv3423c.1	18	2q63_1UN_A_1001 PDB CREDO	0.604	0.174	0.536	0.006
Rv3423c.1	18	2pym_1UN_A_1001 PDB CREDO	0.604	0.174	0.535	0.006
Rv3423c.1	18	2pyn_1UN_A_1001 PDB CREDO	0.602	0.176	0.534	0.006
Rv3423c.1	18	1t7i_017_A_200 PDB CREDO	0.546	0.249	0.534	0.007
Rv3423c.1	9	3fl9_TOP_A_200 PDB CREDO	0.561	0.228	0.533	0.007
Rv3423c.1	9	3grv_ADN_A_300 PDB CREDO	0.617	0.160	0.533	0.007
Rv3423c.1	18	2qxs_RAL_B_600 PDB CREDO	0.719	0.067	0.532	0.007
Rv3423c.1	18	2qxs_RAL_A_600 PDB CREDO	0.719	0.067	0.531	0.007
Rv3423c.1	9	3fl9_TOP_B_200 PDB CREDO	0.557	0.234	0.529	0.007
Rv3423c.1	9	3fl9_TOP_G_200 PDB CREDO	0.555	0.237	0.527	0.007
Rv3423c.1	18	3ndu_ROC_D_100 PDB CREDO	0.551	0.243	0.526	0.007
Rv3423c.1	9	1sn0_T44_B_602 PDB CREDO	0.553	0.239	0.526	0.007
Rv3423c.1	9	3jw3_TOP_A_208 PDB CREDO	0.651	0.124	0.526	0.007
Rv3423c.1	9	1fb7_ROC_A_100 PDB CREDO	0.646	0.128	0.522	0.008
Rv3423c.1	18	3cs9_NIL_B_600 PDB CREDO	0.706	0.076	0.521	0.008
Rv3423c.1	18	1rl8_RIT_A_9001 PDB CREDO	0.574	0.212	0.521	0.008
Rv3423c.1	9	1r9o_FLP_A_501 PDB CREDO	0.631	0.144	0.520	0.008
Rv3423c.1	18	3ogq_AB1_A_200 PDB CREDO	0.616	0.160	0.520	0.008
Rv3423c.1	9	2w9s_TOP_A_1160 PDB CREDO	0.545	0.251	0.518	0.008
Rv3423c.1	9	2w9s_TOP_C_1160 PDB CREDO	0.545	0.251	0.518	0.008
Rv3423c.1	18	3cs9_NIL_A_600 PDB CREDO	0.720	0.066	0.518	0.008
Rv3423c.1	18	3bjw_SVR_B_501 PDB CREDO	0.625	0.150	0.514	0.009
Rv3423c.1	18	3ufn_ROC_A_401 PDB CREDO	0.640	0.135	0.512	0.009
Rv3423c.1	9	1sn0_T44_C_601 PDB CREDO	0.650	0.124	0.512	0.009
Rv3423c.1	18	2nmy_ROC_A_401 PDB CREDO	0.548	0.246	0.512	0.009
Rv3423c.1	18	1opj_STI_A_3 PDB CREDO	0.710	0.074	0.510	0.009
Rv3423c.1	9	2w9g_TOP_A_1159 PDB CREDO	0.598	0.182	0.510	0.009
Rv3423c.1	18	3bjw_SVR_E_503 PDB CREDO	0.672	0.104	0.510	0.009
Rv3423c.1	9	1qhy_CLM_A_999 PDB CREDO	0.536	0.264	0.510	0.009
Rv3423c.1	18	1opj_STI_B_4 PDB CREDO	0.708	0.075	0.509	0.009
Rv3423c.1	18	3gcs_BAX_A_401 PDB CREDO	0.813	0.020	0.507	0.010
Rv3423c.1	9	3fl9_TOP_C_200 PDB CREDO	0.562	0.228	0.506	0.010
Rv3423c.1	18	3bjw_SVR_F_502 PDB CREDO	0.615	0.162	0.505	0.010
Rv3423c.1	18	3bjw_SVR_H_504 PDB CREDO	0.613	0.163	0.504	0.010
Rv3423c.1	18	3el9_DR7_A_100 PDB CREDO	0.664	0.111	0.504	0.010
Rv3423c.1	18	1uwj_BAX_A_1723 PDB CREDO	0.741	0.053	0.504	0.010
Rv3423c.1	18	3pwr_ROC_A_401 PDB CREDO	0.540	0.258	0.503	0.010
Rv3423c.1	18	1hxb_ROC_A_100 PDB CREDO	0.566	0.222	0.502	0.011
Rv3423c.1	18	3cyx_ROC_A_201 PDB CREDO	0.525	0.280	0.501	0.011
Rv3423c.1	18	3oxc_ROC_A_401 PDB CREDO	0.587	0.195	0.501	0.011
Rv3423c.1	9	3hm1_J3Z_A_2 PDB CREDO	0.608	0.170	0.501	0.011
Rv3423c.1	9	3hbb_TMQ_A_611 PDB CREDO	0.579	0.204	0.501	0.011

Similarity to known drug target from sensitive sequence analysis

No drug targets

List of small molecules tested from TIBLE

View results in TIBLE page

Name	Affinity	Assay description	DOI
CDD-1768	None	None	None

Off-target activity - ligand based from TIBLE

View results in TIBLE page

Predicted off-target	Method	Summary	Full results
Retinol-binding protein 4 1RBP	PharmMapper	8 hydroph + 0 HB + 0 pos/neg + 0 arom	Link
Transthyretin 1RLB	PharmMapper	9 hydroph + 1 HB + 0 pos/neg + 0 arom	Link
Beta-secretase 1 2G94	PharmMapper	5 hydroph + 10 HB + 0 pos/neg + 0 arom	Link
Cellular retinoic acid-binding protein 2 1CBS	PharmMapper	7 hydroph + 2 HB + 1 pos/neg + 0 arom	Link
Cellular retinoic acid-binding protein 2 3CBS	PharmMapper	6 hydroph + 2 HB + 1 pos/neg + 0 arom	Link
alpha-glucosidase [-]	SEA	E_value = 4.26e-31 & MaxTC = 0.61	Link

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
pyridoxal phosphatePubChem	0.995	247.142
D-alaninePubChem	0.991	89.0932
L-alaninePubChem	0.99	89.0932
D-cycloserinePubChem	0.988	102.092
L-valinePubChem	0.923	117.146
ammoniaPubChem	0.919	17.0305
alpha-ketoglutaratePubChem	0.917	146.098
glutamatePubChem	0.917	147.129
hydroxyl radicalsPubChem	0.91	17.0073
ubiquinol-1PubChem	0.9	252.306
pyruvic acidPubChem	0.9	88.0621
ubiquinonesPubChem	0.9	250.29
cysteinatePubChem	0.9	121.158
alpha-ketoisovaleratePubChem	0.9	116.115
ubiquinolPubChem	0.9	320.423
half-cystinePubChem	0.9	121.158
CoQPubChem	0.9	318.407
propionatePubChem	0.816	74.0785
DB03787PubChem	0.743	333.234
iminesPubChem	0.733	29.0412