SInCRe - Rv1415

Tuberculist information

Gene name	ribA2
Protein function	Probable riboflavin biosynthesis protein RibA2 : GTP cyclohydrolase II + 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase)
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	1590.4
Molecular mass(da)	46017.3
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 425

	  		  	1    MTRLDSVERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVP   60
			  	61   LDGAICDRLGLLPMYAVNQDKHGTAYTVTVDARNGIGTGISASDRATTMRLLADPTSVAD  120
			  	121  DFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDE  180
			  	181  LRVFADEHGLALITIADLIEWRRKHEKHIERVAEARIPTRHGEFRAIGYTSIYEDVEHVA  240
			  	241  LVRGEIAGPNADGDDVLVRVHSECLTGDVFGSRRCDCGPQLDAALAMVAREGRGVVLYMR  300
			  	301  GHEGRGIGLMHKLQAYQLQDAGADTVDANLKLGLPADARDYGIGAQILVDLGVRSMRLLT  360
			  	361  NNPAKRVGLDGYGLHIIERVPLPVRANAENIRYLMTKRDKLGHDLAGLDDFHESVHLPGE  420
			  	421  FGGAL

Known structures in the PDB

	PDB ID	3MGZ
	Total residue count	206
	Number of chains	1
	Method	X-RAY
	Resolution	2.07

	PDB ID	3MIO
	Total residue count	412
	Number of chains	2
	Method	X-RAY
	Resolution	1.8

	PDB ID	3MK5
	Total residue count	212
	Number of chains	1
	Method	X-RAY
	Resolution	2.06

	PDB ID	4I14
	Total residue count	850
	Number of chains	2
	Method	X-RAY
	Resolution	3

Number of amino acids : 425

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
DHBP_synthase	PF00926	7-202
GTP_cyclohydro2	PF00925	209-382

Mtb Structural Proteome models

Model Number	1
Model name	Rv1415
Template	1TKS APDB CREDO
Template coverage	5_201
Template Identity(%)	53.4
Model coverage(%)	46.4
Normalized DOPE score	-1.357

Model Number	2
Model name	Rv1415.3
Template	2BZ1 APDB CREDO
Template coverage	2_174
Template Identity(%)	54.3
Model coverage(%)	41.6
Normalized DOPE score	-0.87

Structure Models from Chopin

Model Number	1
Profile	c.144.1.1 Click for model details
zscore	47.29
Residue begin	209
Residue end	382

Model Number	2
Profile	d.115.1.2 - 3.90.870.10 Click for model details
zscore	46.4
Residue begin	7
Residue end	202

Binding pockets

STRING

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

Protein interacting with Rv1415	Gene name	Confidence Score
Rv1409	ribG	0.999
Rv1409	ribG	0.999
Rv1416	ribH	0.999
Rv1412	ribC	0.996
Rv2671	ribD	0.976

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv1415.3	7	4dta_ADN_A_401 PDB CREDO	0.611	0.166	0.585	0.003
Rv1415.3	7	1pg2_ADN_A_552 PDB CREDO	0.623	0.152	0.544	0.006
Rv1415.3	7	3lfa_1N1_A_361 PDB CREDO	0.587	0.194	0.539	0.006
Rv1415.3	7	2y7j_B49_D_1294 PDB CREDO	0.561	0.229	0.536	0.006
Rv1415.3	7	4dt8_ADN_A_401 PDB CREDO	0.548	0.246	0.525	0.007
Rv1415.3	7	2y7j_B49_B_1294 PDB CREDO	0.602	0.177	0.509	0.010
Rv1415.3	7	1uay_ADN_A_1001 PDB CREDO	0.555	0.237	0.507	0.010
Rv1415.3	7	1xwf_ADN_B_433 PDB CREDO	0.525	0.280	0.502	0.011
Rv1415.3	7	1xwf_ADN_D_433 PDB CREDO	0.525	0.280	0.502	0.011
Rv1415.3	7	2x1l_ADN_C_601 PDB CREDO	0.524	0.281	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
ribulose 5-phosphatePubChem	0.985	230.11
3,4-dihydroxy-2-butanone 4-phosphatePubChem	0.976	184.084
ribulose-5-phosphatePubChem	0.971	230.11
guanosine triphosphatePubChem	0.943	523.18
formatePubChem	0.936	45.0174
pyrophosphatePubChem	0.92	177.975
deuteriumPubChem	0.9	2.01588
ammoniaPubChem	0.9	17.0305
hydroxyl radicalsPubChem	0.9	17.0073
C01268PubChem	0.9	354.211
H(+)PubChem	0.9	2.01588
protiumPubChem	0.9	2.01576
C01304PubChem	0.9	353.226
zincPubChem	0.831	65.409
riboflavinPubChem	0.775	376.364
glycerolPubChem	0.738	92.0938