SInCRe - Rv1570

Tuberculist information

Gene name	bioD
Protein function	Dethiobiotin synthetase BioD
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	1777.86
Molecular mass(da)	22437.9
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 226

	  		  	1    LTILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDDDLAEVGRLAGVT   60
			  	61   QLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADLDRPGRLTLVEGAGGLLVELAEP  120
			  	121  GVTLRDVAVDVAAAALVVVTADLGTLNHTKLTLEALAAQQVSCAGLVIGSWPDPPGLVAA  180
			  	181  SNRSALARIAMVRAALPAGAASLDAGDFAAMSAAAFDRNWVAGLVG

Known structures in the PDB

	PDB ID	3FGN
	Total residue count	1004
	Number of chains	4
	Method	X-RAY
	Resolution	1.85

	PDB ID	3FMF
	Total residue count	1004
	Number of chains	4
	Method	X-RAY
	Resolution	2.05

	PDB ID	3FMI
	Total residue count	1004
	Number of chains	4
	Method	X-RAY
	Resolution	2.18

	PDB ID	3FPA
	Total residue count	1004
	Number of chains	4
	Method	X-RAY
	Resolution	2.3

Number of amino acids : 226

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
AAA_26	PF13500	2-199

Mtb Structural Proteome models

Model Number	1
Model name	Rv1570_3fgn_A
Template	3FGN APDB CREDO
Template coverage	0_226
Template Identity(%)	100.0
Model coverage(%)	100.0
Normalized DOPE score	-1.352

Model Number	2
Model name	Rv1570
Template	1BYI APDB CREDO
Template coverage	2_224
Template Identity(%)	25.9
Model coverage(%)	96.9
Normalized DOPE score	-0.08

Structure Models from Chopin

Model Number	1
Profile	c.37.1.10 - 3.40.50.300 Click for model details
zscore	14.45
Residue begin	1
Residue end	226

Binding pockets

STRING

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

Protein interacting with Rv1570	Gene name	Confidence Score
Rv1568	bioA	0.999
Rv1589	bioB	0.999
Rv1589	bioB	0.999
Rv1569	bioF1	0.995
Rv1571	Rv1571	0.949
Rv2753c	dapA	0.912

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv1570_3fgn_A	1	1hwk_117_D_3 PDB CREDO	0.603	0.176	0.585	0.003
Rv1570_3fgn_A	1	1hwi_115_D_3 PDB CREDO	0.601	0.178	0.582	0.003
Rv1570_3fgn_A	1	1hwi_115_B_1 PDB CREDO	0.599	0.181	0.580	0.003
Rv1570_3fgn_A	1	1hwl_FBI_D_3 PDB CREDO	0.613	0.163	0.577	0.003
Rv1570_3fgn_A	1	1hwl_FBI_B_1 PDB CREDO	0.613	0.164	0.576	0.003
Rv1570_3fgn_A	1	1hwl_FBI_C_4 PDB CREDO	0.610	0.168	0.573	0.003
Rv1570_3fgn_A	1	1hwl_FBI_A_2 PDB CREDO	0.609	0.168	0.573	0.003
Rv1570_3fgn_A	1	1hwk_117_A_2 PDB CREDO	0.625	0.150	0.571	0.004
Rv1570_3fgn_A	1	1hwk_117_C_4 PDB CREDO	0.625	0.150	0.571	0.004
Rv1570_3fgn_A	1	1hwk_117_B_1 PDB CREDO	0.662	0.113	0.570	0.004
Rv1570_3fgn_A	1	3tne_RIT_A_401 PDB CREDO	0.586	0.196	0.568	0.004
Rv1570_3fgn_A	1	1hwi_115_A_2 PDB CREDO	0.642	0.132	0.565	0.004
Rv1570_3fgn_A	1	3tne_RIT_B_401 PDB CREDO	0.582	0.201	0.564	0.004
Rv1570_3fgn_A	1	3ut5_LOC_D_502 PDB CREDO	0.574	0.211	0.557	0.004
Rv1570_3fgn_A	1	3ut5_LOC_B_502 PDB CREDO	0.570	0.217	0.552	0.005
Rv1570_3fgn_A	1	3spk_TPV_B_100 PDB CREDO	0.623	0.152	0.552	0.005
Rv1570_3fgn_A	1	3q70_RIT_A_2001 PDB CREDO	0.573	0.213	0.539	0.006
Rv1570_3fgn_A	1	3spk_TPV_A_100 PDB CREDO	0.630	0.145	0.536	0.006
Rv1570_3fgn_A	1	1sa1_POD_D_701 PDB CREDO	0.569	0.218	0.536	0.006
Rv1570_3fgn_A	1	1sa1_POD_B_700 PDB CREDO	0.585	0.197	0.534	0.006
Rv1570_3fgn_A	1	3so9_017_A_100 PDB CREDO	0.537	0.262	0.521	0.008
Rv1570_3fgn_A	1	1hwi_115_C_4 PDB CREDO	0.652	0.122	0.518	0.008
Rv1570_3fgn_A	1	1uwh_BAX_A_1723 PDB CREDO	0.534	0.267	0.518	0.008
Rv1570_3fgn_A	1	1uwh_BAX_B_1723 PDB CREDO	0.534	0.267	0.518	0.008
Rv1570_3fgn_A	1	1t7j_478_A_200 PDB CREDO	0.534	0.267	0.517	0.008
Rv1570_3fgn_A	1	3tkd_CYZ_A_266 PDB CREDO	0.530	0.272	0.514	0.009
Rv1570_3fgn_A	1	2y6o_1N1_A_1892 PDB CREDO	0.546	0.250	0.512	0.009
Rv1570_3fgn_A	1	1jg2_ADN_A_500 PDB CREDO	0.644	0.131	0.512	0.009
Rv1570_3fgn_A	1	2nni_MTK_A_501 PDB CREDO	0.576	0.209	0.511	0.009
Rv1570_3fgn_A	1	1uwj_BAX_A_1723 PDB CREDO	0.609	0.168	0.510	0.009
Rv1570_3fgn_A	1	3tkd_CYZ_B_267 PDB CREDO	0.525	0.281	0.509	0.010
Rv1570_3fgn_A	1	1uwj_BAX_B_1723 PDB CREDO	0.550	0.243	0.503	0.010

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
dethiobiotinPubChem	0.996	214.262
7-keto-8-aminopelargonic acidPubChem	0.995	187.236
DTBPubChem	0.99	214.262
phosphatePubChem	0.989	96.9872
7,8-diaminopelargonic acidPubChem	0.958	188.267
DB03624PubChem	0.9	232.277
hydron sulfatePubChem	0.9	196.157
deuteriumPubChem	0.9	2.01588
8-amino-7-oxononanoic acidPubChem	0.9	187.236
magnesiumPubChem	0.9	24.305
H(+)PubChem	0.9	2.01588
adenosine triphosphatePubChem	0.9	507.181
S-adenosyl-4-methylthio-2-oxobutanoatePubChem	0.9	398.414
protiumPubChem	0.9	2.01576
carbon dioxidePubChem	0.9	44.0095
sulfatePubChem	0.9	96.0626
hydron diphosphatePubChem	0.9	391.981
5'-deoxyadenosinePubChem	0.9	251.242
L-methioninePubChem	0.9	149.211
7,8-diaminononanoic acidPubChem	0.9	188.267
adenosine diphosphatePubChem	0.9	427.201
d-biotinPubChem	0.9	244.311
S-adenosyl-L-methioninePubChem	0.9	399.445
S-adenosyl-methioninePubChem	0.9	398.437