Rv2753c

Tuberculist information
Gene namedapA
Protein functionProbable dihydrodipicolinate synthase DapA (DHDPS) (dihydrodipicolinate synthetase)
Functional category(tuberculist)intermediary metabolism and respiration
Gene location(kb)3066.22
Molecular mass(da)30826.2
External sites TB Database TubercuList WebTB
Protein sequence
Number of amino acids : 300
	  		  	1    VTTVGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPT   60
			  	61   TTDGEKIELLRAVLEAVGDRARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKP  120
			  	121  PQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRALASHPNIVGVKDAKADLHSG  180
			  	181  AQIMADTGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKI  240
			  	241  NIAVAPLCNAMSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR  300

Known structures in the PDB
PDB ID1XXX
Total residue count2424
Number of chains8
MethodX-RAY
Resolution2.28
PDB ID3L21
Total residue count1824
Number of chains6
MethodX-RAY
Resolution2.1
1 31 61 91 121 151 181 211 241 271 301 Range: 11 to 297  |  Coverage: 95% DHDPS Range: 5 to 300  |  Coverage: 98% 1 Range: 1 to 300  |  Coverage: 99% 1
Number of amino acids : 300
Domains assigned based on sequence. Mtb Structural proteome models CHOPIN models
Profile-based domain assignment
Structural/Functional domain familyPfam acc.no./SCOP IDDomain Region
DHDPSPF0070111-297
Mtb Structural Proteome models
Model Number1
Model nameRv2753c
Template1XXX    APDBCREDO
Template coverage5_300
Template Identity(%)100.0
Model coverage(%)98.3
Normalized DOPE score-1.739

Structure Models from Chopin
Model Number1
Profilec.1.10.1 - 3.20.20.70
Click for model details
zscore19.56
Residue begin1
Residue end300
Binding pockets
STRING
Cytoscape Web will replace the contents of this div with protein-protein interaction network.
Protein interacting with Rv2753cGene nameConfidence Score
Rv2773cdapB0.999
Rv2773cdapB0.999
Rv3708casd0.998
Rv3708casd0.998
Rv2726cdapF0.994
Rv1293lysA0.99
Rv1293lysA0.99
Rv1294thrA0.981
Rv1294thrA0.981
Rv1294thrA0.981
Rv2752cRv2752c0.979
Rv2752cRv2752c0.979
Rv3709cask0.973
Rv3709cask0.973
Rv3709cask0.973
Rv1568bioA0.95
Rv2785crpsO0.934
Rv1202dapE0.932
Rv1202dapE0.932
Rv2925crnc0.922
Rv2925crnc0.922
Rv2540caroF0.922
Rv1655argD0.913
Rv1569bioF10.912
Rv1570bioD0.912
Rv2906ctrmD0.91
Rv1559ilvA0.909
Rv1559ilvA0.909
Rv2890crpsB0.902
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
CHEMBL124513Inhibition = 43 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL2096741Inhibition = 14 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL2096896Inhibition = 1 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL252909Inhibition = 73 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL255577Inhibition = 0 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL257463Inhibition = 6 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL271858Inhibition = 84 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL272291Inhibition = 0 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL284104Inhibition = 75 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL307925Inhibition = 24 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL401506Inhibition = 7 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL403413Inhibition = 0 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CHEMBL72405Inhibition = 0 %Inhibition of Mycobacterium tuberculosis DHDPS at 20 mMhttp://www.ncbi.nlm.nih.gov/pubmed/18054225
CDD-341648NoneNoneNone
Off-target activity - ligand based from TIBLE
  View results in TIBLE page
Predicted off-targetMethodSummaryFull results
Ras-related protein Rab-5A 1TU4PharmMapper0 hydroph + 10 HB + 0 pos/neg + 0 aromLink
3 histone mRNA exonuclease 1 1W0HPharmMapper0 hydroph + 9 HB + 1 pos/neg + 0 aromLink
Inosine-5-monophosphate dehydrogenase 2 1NFBPharmMapper0 hydroph + 8 HB + 0 pos/neg + 1 aromLink
Tyrosine-protein phosphatase non-receptor type 1 1JF7PharmMapper2 hydroph + 6 HB + 2 pos/neg + 0 aromLink
Ras-related protein Rap-2a 1KAOPharmMapper0 hydroph + 12 HB + 2 pos/neg + 0 aromLink
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
chloridePubChem0.97935.453
dihydrodipicolinatePubChem0.977169.135
pyruvic acidPubChem0.97788.0621
magnesiumPubChem0.97724.305
phosphatePubChem0.97796.9872
L-aspartate-beta-semialdehydePubChem0.975117.103
delta1-piperideine-2,6-dicarboxylatePubChem0.956171.151
L-lysinePubChem0.933146.188
7-keto-8-aminopelargonic acidPubChem0.924187.236
7,8-diaminopelargonic acidPubChem0.921188.267
beta-aspartyl phosphatePubChem0.9213.083
dithiothreitolPubChem0.9154.251
deuteriumPubChem0.92.01588
L-2,3,4,5-tetrahydrodipicolinatePubChem0.9171.151
NADP(H)PubChem0.9745.421
H(+)PubChem0.92.01588
protiumPubChem0.92.01576
threo-1,4-dimercapto-2,3-butanediolPubChem0.9154.251
NADPPubChem0.9744.413
hydroxyl radicalsPubChem0.917.0073
aspartyl phosphatePubChem0.9213.083
amiclenomycinPubChem0.891196.246
diaminopimelic acidPubChem0.847190.197
DTBPubChem0.83214.262
thialysinePubChem0.817200.687
dethiobiotinPubChem0.813214.262
glycerolPubChem0.80692.0938
N(epsilon)-(carboxyethyl)lysinePubChem0.797218.25
DB02370PubChem0.797218.25
8-amino-7-oxononanoic acidPubChem0.792187.236
hydron sulfatePubChem0.786196.157
sulfatePubChem0.78696.0626
Na(+)PubChem0.77822.9898
8-amino-7-oxooctanoic acidPubChem0.762174.218
meso-diaminopimelatePubChem0.762190.197
polyethylene glycolPubChem0.75862.0678
hydron diphosphatePubChem0.757391.981
(R)-KAPAPubChem0.755187.236
potassiumPubChem0.74539.0983
SeMetPubChem0.743196.106
selenomethioninePubChem0.743196.106
potassium hydridePubChem0.74240.1062
sinefunginPubChem0.733381.387
hydroxypyruvatePubChem0.73104.061
calciumPubChem0.71440.078
S-adenosyl-L-methioninePubChem0.706398.437