Rv2682c

Tuberculist information
Gene namedxs1
Protein functionProbable 1-deoxy-D-xylulose 5-phosphate synthase Dxs1 (1-deoxyxylulose-5-phosphate synthase) (DXP synthase) (DXPS)
Functional category(tuberculist)intermediary metabolism and respiration
Gene location(kb)2998.05
Molecular mass(da)67885.4
External sites TB Database TubercuList WebTB
Protein sequence
Number of amino acids : 638
	  		  	1    MLQQIRGPADLQHLSQAQLRELAAEIREFLIHKVAATGGHLGPNLGVVELTLALHRVFDS   60
			  	61   PHDPIIFDTGHQAYVHKMLTGRSQDFATLRKKGGLSGYPSRAESEHDWVESSHASAALSY  120
			  	121  ADGLAKAFELTGHRNRHVVAVVGDGALTGGMCWEALNNIAASRRPVIIVVNDNGRSYAPT  180
			  	181  IGGVADHLATLRLQPAYEQALETGRDLVRAVPLVGGLWFRFLHSVKAGIKDSLSPQLLFT  240
			  	241  DLGLKYVGPVDGHDERAVEVALRSARRFGAPVIVHVVTRKGMGYPPAEADQAEQMHSTVP  300
			  	301  IDPATGQATKVAGPGWTATFSDALIGYAQKRRDIVAITAAMPGPTGLTAFGQRFPDRLFD  360
			  	361  VGIAEQHAMTSAAGLAMGGLHPVVAIYSTFLNRAFDQIMMDVALHKLPVTMVLDRAGITG  420
			  	421  SDGASHNGMWDLSMLGIVPGIRVAAPRDATRLREELGEALDVDDGPTALRFPKGDVGEDI  480
			  	481  SALERRGGVDVLAAPADGLNHDVLLVAIGAFAPMALAVAKRLHNQGIGVTVIDPRWVLPV  540
			  	541  SDGVRELAVQHKLLVTLEDNGVNGGAGSAVSAALRRAEIDVPCRDVGLPQEFYEHASRSE  600
			  	601  VLADLGLTDQDVARRITGWVAALGTGVCASDAIPEHLD

Known structures in the PDB
PDB ID4JDY
Total residue count792
Number of chains3
MethodX-RAY
Resolution1.8
1 64 127 190 253 316 379 442 505 568 631 Range: 2 to 278  |  Coverage: 43% DXP_synthase_N Range: 312 to 479  |  Coverage: 26% Transket_pyr Range: 493 to 612  |  Coverage: 18% Transketolase_C Range: 19 to 628  |  Coverage: 95% 1 Range: 1 to 638  |  Coverage: 99% 1 Range: 312 to 479  |  Coverage: 26% 2 Range: 493 to 612  |  Coverage: 18% 3 Range: 480 to 638  |  Coverage: 24% 4 Range: 304 to 624  |  Coverage: 50% 5 Range: 2 to 362  |  Coverage: 56% 6
Number of amino acids : 638
Domains assigned based on sequence. Mtb Structural proteome models CHOPIN models
Profile-based domain assignment
Structural/Functional domain familyPfam acc.no./SCOP IDDomain Region
DXP_synthase_NPF132922-278
Transket_pyrPF02779312-479
Transketolase_CPF02780493-612
Mtb Structural Proteome models
Model Number1
Model nameRv2682c
Template1R9J    APDBCREDO
Template coverage4_661
Template Identity(%)17.5
Model coverage(%)95.5
Normalized DOPE score0.286

Structure Models from Chopin
Model Number1
Profilec.36.1.10, c.36.1.6, c.48.1.1
Click for model details
zscore29.46
Residue begin1
Residue end638
Model Number2
Profilec.36.1.6
Click for model details
zscore23.93
Residue begin312
Residue end479
Model Number3
Profilec.48.1.2
Click for model details
zscore18.58
Residue begin493
Residue end612
Model Number4
Profile3.40.50.920
Click for model details
zscore17.58
Residue begin480
Residue end638
Model Number5
Profilec.36.1.7, c.48.1.2 - 3.40.50.920, 3.40.50.970
Click for model details
zscore13.48
Residue begin304
Residue end624
Model Number6
Profilec.36.1.10
Click for model details
zscore12.82
Residue begin2
Residue end362
Binding pockets
STRING
Cytoscape Web will replace the contents of this div with protein-protein interaction network.
Protein interacting with Rv2682cGene nameConfidence Score
Rv2870cdxr0.999
Rv2870cdxr0.999
Rv2870cdxr0.999
Rv2868cgcpE0.99
Rv0417thiG0.986
Rv3581cispF0.981
Rv1110lytB20.972
Rv3582cispD0.966
Rv0422cthiD0.964
Rv1011ispE0.964
Rv1011ispE0.964
Rv1745cidi0.956
Rv0414cthiE0.91
Rv1696recN0.901
Potential ligand/drug binding sites
No binding sites identified
Similarity to known drug target from sensitive sequence analysis
No drug targets
List of small molecules tested from TIBLE
  View results in TIBLE page
NameAffinityAssay descriptionDOI
CHEMBL476980IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL488964IC50 = 63.7 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL489164IC50 = 34.2 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL489173IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL489785IC50 = 55.1 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL490176IC50 = 71.1 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491194IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491195IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491196IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491210IC50 = 10.6 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491211IC50 = 30.6 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491216IC50 = 19.5 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491391IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491398IC50 = 73 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491399IC50 = 98.4 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL491607IC50 = 10.9 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL505210IC50 = 114.1 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL505602IC50 = 42.4 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL507286IC50 = 19.7 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL514373IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL521577IC50 = 14 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL521592IC50 = 41.4 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL522297IC50 = 20.2 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL522461IC50 = 53.5 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL522583IC50 = 90.7 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL522627IC50 = 17.9 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL522818IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL522946IC50 = 23 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
CHEMBL523980IC50 > 200 uMInhibition of Mycobacterium tuberculosis cloned 1-deoxy-D-xylulose-5-phosphate synthase expressed in Escherichia colihttp://www.ncbi.nlm.nih.gov/pubmed/18783951
Off-target activity - ligand based from TIBLE
  View results in TIBLE page
Predicted off-targetMethodSummaryFull results
Cellular retinoic acid-binding protein 2 1CBSPharmMapper7 hydroph + 2 HB + 1 pos/neg + 0 aromLink
Beta-secretase 1 1TQFPharmMapper5 hydroph + 3 HB + 1 pos/neg + 0 aromLink
Transthyretin 1RLBPharmMapper9 hydroph + 1 HB + 0 pos/neg + 0 aromLink
3-phosphoinositide-dependent protein kinase 1 2PE1PharmMapper3 hydroph + 4 HB + 0 pos/neg + 0 aromLink
Mitogen-activated protein kinase 14 1ZZLPharmMapper4 hydroph + 3 HB + 0 pos/neg + 0 aromLink
GABA receptor gamma-2 subunit SEAE_value = 5.44e-11 & MaxTC = 0.44Link
GABA receptor beta-1 subunit SEAE_value = 5.44e-11 & MaxTC = 0.44Link
Small molecules involved in protein-protein complex from TIMBAL .Proteins similar to Mtb based on sequence analysis.
Data not available
STITCH interactions  
Chemical NameConfidence scoreMolecular Weight
1-deoxy-D-xylulose 5-phosphatePubChem0.99214.11
D-glyceraldehyde-3-phosphatePubChem0.968170.058
phosphatePubChem0.92896.9872
thiamine pyrophosphatePubChem0.918425.314
glyceraldehyde-3-phosphatePubChem0.916170.058
deuteriumPubChem0.9022.01588
dehydroglycinePubChem0.973.0507
protiumPubChem0.92.01576
hydroxyl radicalsPubChem0.917.0073
4-hydroxybenzyl alcoholPubChem0.9124.137
pyridoxine 5'-phosphatePubChem0.9249.158
H(+)PubChem0.92.01588
3-amino-2-oxopropyl phosphatePubChem0.9169.073
carbon dioxidePubChem0.944.0095
pyruvic acidPubChem0.988.0621
4-methyl-5-(beta-hydroxyethyl)thiazole phosphatePubChem0.9223.187
isopentenyl diphosphatePubChem0.86246.092
mevalonatePubChem0.745148.157
magnesiumPubChem0.73324.305