SInCRe - Rv0462

Tuberculist information

Gene name	lpdC
Protein function	Dihydrolipoamide dehydrogenase LpdC (lipoamide reductase (NADH)) (lipoyl dehydrogenase) (dihydrolipoyl dehydrogenase) (diaphorase)
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	552.614
Molecular mass(da)	49207.1
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 464

	  		  	1    VTHYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVH   60
			  	61   IFTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANT  120
			  	121  LLVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAG  180
			  	181  AIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIAD  240
			  	241  GGSQVTVTVTKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRTN  300
			  	301  VGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFGL  360
			  	361  TEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAELL  420
			  	421  PELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMINF

Known structures in the PDB

	PDB ID	2A8X
	Total residue count	928
	Number of chains	2
	Method	X-RAY
	Resolution	2.4

	PDB ID	3II4
	Total residue count	932
	Number of chains	2
	Method	X-RAY
	Resolution	2.42

	PDB ID	4M52
	Total residue count	1864
	Number of chains	4
	Method	X-RAY
	Resolution	2.4

Number of amino acids : 464

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
Pyr_redox_2	PF07992	5-313
Pyr_redox	PF00070	173-253
Pyr_redox_dim	PF02852	345-454

Mtb Structural Proteome models

Model Number	1
Model name	Rv0462_3ii4_A
Template	3II4 APDB CREDO
Template coverage	2_464
Template Identity(%)	100.0
Model coverage(%)	99.6
Normalized DOPE score	-1.054

Model Number	2
Model name	Rv0462
Template	2A8X APDB CREDO
Template coverage	1_464
Template Identity(%)	100.0
Model coverage(%)	99.8
Normalized DOPE score	-0.838

Structure Models from Chopin

Model Number	1
Profile	c.3.1.5, d.87.1.1 Click for model details
zscore	79.3
Residue begin	1
Residue end	464

Model Number	2
Profile	d.87.1.1 Click for model details
zscore	14.01
Residue begin	345
Residue end	454

Model Number	3
Profile	d.87.1.1 Click for model details
zscore	11.76
Residue begin	284
Residue end	464

Model Number	4
Profile	c.3.1.5 Click for model details
zscore	11.4
Residue begin	126
Residue end	273

Binding pockets

STRING

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

Protein interacting with Rv0462	Gene name	Confidence Score
Rv2215	dlaT	0.999
Rv2215	dlaT	0.999
Rv2215	dlaT	0.999
Rv2495c	bkdC	0.998
Rv2495c	bkdC	0.998
Rv2495c	bkdC	0.998
Rv2496c	bkdB	0.998
Rv2496c	bkdB	0.998
Rv2497c	bkdA	0.996
Rv2241	aceE	0.995
Rv1248c	Rv1248c	0.993
Rv1248c	Rv1248c	0.993
Rv1248c	Rv1248c	0.993
Rv1832	gcvB	0.985
Rv1832	gcvB	0.985
Rv2429	ahpD	0.983
Rv0843	Rv0843	0.98
Rv2211c	gcvT	0.978
Rv2211c	gcvT	0.978
Rv2217	lipB	0.954
Rv0951	sucC	0.942
Rv0951	sucC	0.942
Rv1437	pgk	0.924
Rv1023	eno	0.915
Rv1023	eno	0.915
Rv0752c	fadE9	0.912
Rv0752c	fadE9	0.912
Rv1826	gcvH	0.912
Rv0752c	fadE9	0.912
Rv1617	pykA	0.911
Rv1617	pykA	0.911

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv0462_3ii4_A	4	2v0z_C41_C_1328 PDB CREDO	0.753	0.046	0.595	0.002
Rv0462_3ii4_A	4	3sm2_478_A_126 PDB CREDO	0.742	0.052	0.585	0.003
Rv0462_3ii4_A	4	2v0z_C41_O_1327 PDB CREDO	0.792	0.028	0.579	0.003
Rv0462_3ii4_A	4	3kk6_CEL_A_701 PDB CREDO	0.741	0.053	0.556	0.005
Rv0462_3ii4_A	4	1xkk_FMM_A_91 PDB CREDO	0.706	0.076	0.529	0.007
Rv0462_3ii4_A	4	3prs_RIT_A_1001 PDB CREDO	0.614	0.163	0.509	0.010
Rv0462_3ii4_A	4	2aof_FRD_C_305 PDB CREDO	0.555	0.236	0.507	0.010
Rv0462_3ii4_A	4	3bjw_SVR_B_501 PDB CREDO	0.670	0.106	0.502	0.011
Rv0462_3ii4_A	4	1ya4_CTX_A_1 PDB CREDO	0.590	0.191	0.501	0.011
Rv0462_3ii4_A	4	3bjw_SVR_H_504 PDB CREDO	0.668	0.108	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
lipoamidePubChem	0.988	205.341
flavin adenine dinucleotidePubChem	0.983	785.55
NAD+PubChem	0.977	663.425
dihydrolipoamidePubChem	0.96	207.357
acetyl-CoAPubChem	0.948	809.571
reduced nicotinamide adenine dinucleotidePubChem	0.943	665.441
H(+)PubChem	0.929	2.01588
deuteriumPubChem	0.927	2.01588
DL-lipoamidePubChem	0.914	205.341
pyruvic acidPubChem	0.913	88.0621
coenzyme APubChem	0.913	767.534
carbon dioxidePubChem	0.904	44.0095
2-methyl-2,4-pentanediolPubChem	0.903	118.174
(4s)-2-Methyl-2,4-PentanediolPubChem	0.903	118.174
selenomethioninePubChem	0.901	196.106
SeMetPubChem	0.901	196.106
Co-APubChem	0.9	767.534
3IIPubChem	0.9	625.542
LPMPubChem	0.9	207.357
protiumPubChem	0.9	2.01576
acetyl coenzyme-APubChem	0.9	809.571
dihydronicotinamide formycin dinucleotidePubChem	0.9	665.441