Rv0548c

Tuberculist information
Gene namemenB
Protein functionNaphthoate synthase MenB (dihydroxynaphthoic acid synthetase) (DHNA synthetase)
Functional category(tuberculist)intermediary metabolism and respiration
Gene location(kb)639.012
Molecular mass(da)34656.9
External sites TB Database TubercuList WebTB
Protein sequence
Number of amino acids : 314
	  		  	1    VVAPAGEQGRSSTALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNA   60
			  	61   FRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASG  120
			  	121  DTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYAR  180
			  	181  FKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELE  240
			  	241  TVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGRDAFL  300
			  	301  QKRPPDWSPFPRYF

Known structures in the PDB
PDB ID1Q51
Total residue count3768
Number of chains12
MethodX-RAY
Resolution2.3
PDB ID1Q52
Total residue count3768
Number of chains12
MethodX-RAY
Resolution1.8
PDB ID1RJM
Total residue count1017
Number of chains3
MethodX-RAY
Resolution2.15
PDB ID1RJN
Total residue count1017
Number of chains3
MethodX-RAY
Resolution2.3
PDB ID3T8A
Total residue count1002
Number of chains3
MethodX-RAY
Resolution2.24
PDB ID3T8B
Total residue count668
Number of chains2
MethodX-RAY
Resolution1.65
1 32 63 94 125 156 187 218 249 280 311 Range: 40 to 302  |  Coverage: 83% ECH Range: 18 to 314  |  Coverage: 94% 1 Range: 18 to 314  |  Coverage: 94% 2 Range: 1 to 314  |  Coverage: 99% 1 Range: 252 to 312  |  Coverage: 19% 2
Number of amino acids : 314
Domains assigned based on sequence. Mtb Structural proteome models CHOPIN models
Profile-based domain assignment
Structural/Functional domain familyPfam acc.no./SCOP IDDomain Region
ECHPF0037840-302
Mtb Structural Proteome models
Model Number1
Model nameRv0548c_1q52_A
Template1Q52    APDBCREDO
Template coverage18_314
Template Identity(%)100.0
Model coverage(%)94.3
Normalized DOPE score-1.398

Model Number2
Model nameRv0548c
Template1Q52    APDBCREDO
Template coverage18_314
Template Identity(%)100.0
Model coverage(%)94.3
Normalized DOPE score-0.763

Structure Models from Chopin
Model Number1
Profilec.14.1.3 - 3.90.226.10
Click for model details
zscore29.73
Residue begin1
Residue end314
Model Number2
Profile1.10.12.10
Click for model details
zscore10.32
Residue begin252
Residue end312
Binding pockets
STRING
Cytoscape Web will replace the contents of this div with protein-protein interaction network.
Protein interacting with Rv0548cGene nameConfidence Score
Rv0555menD0.998
Rv0555menD0.998
Rv0542cmenE0.98
Rv0542cmenE0.98
Rv0553menC0.976
Rv0553menC0.976
Rv0534cmenA0.964
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
CHEMBL2024251Not ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA up to 300 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024253IC50 = 52.7 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenE preincubated for 1 hrhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024253IC50 > 120 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024254IC50 > 120 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024254IC50 = 14.4 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenE preincubated for 1 hrhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024255IC50 = 11.7 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenE preincubated for 1 hrhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024255IC50 > 120 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024256IC50 > 120 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024256IC50 = 8.4 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenE preincubated for 1 hrhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024257IC50 = 3.2 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenE preincubated for 1 hrhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024257IC50 > 120 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024258IC50 > 120 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenE preincubated for 1 hrhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024258IC50 > 120 uMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024259Not ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024260Not ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024261Not ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024262Not ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024263Not ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024264Not ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024265ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024334ActiveInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024335IC50 = 468 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024335Ki = 350 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by Lineweaver-Burk plot analysishttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024335Ki = 1630 nMNon-competitive inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by Lineweaver-Burk plot analysishttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024336IC50 = 33500 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024337IC50 = 204 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024338IC50 = 103 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024338Ki = 792 nMNon-competitive inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by Lineweaver-Burk plot analysishttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024338Ki = 97 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by Lineweaver-Burk plot analysishttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024339IC50 = 135 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024340IC50 = 421 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024341IC50 = 154 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024342IC50 = 12100 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024343IC50 = 14100 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024344Ki = 286 nMNon-competitive inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by Lineweaver-Burk plot analysishttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024344Ki = 49 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by Lineweaver-Burk plot analysishttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024344IC50 = 106 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024345IC50 = 2200 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
CHEMBL2024346IC50 > 400000 nMInhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenEhttp://dx.doi.org/10.1021/ml200141e
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 NameConfidence scoreMolecular Weight
coenzyme APubChem0.996767.534
acetoacetyl-CoAPubChem0.994851.607
Co-APubChem0.989767.534
1,4-dihydroxy-2-naphthoic acidPubChem0.982204.179
4-(2'-carboxyphenyl)-4-oxobutyric acidPubChem0.98222.194
1,4-dihydroxy-2-naphthoyl-CoAPubChem0.979953.698
o-succinylbenzoyl-CoAPubChem0.972971.713
acetoacetyl-coenzyme APubChem0.961851.607
adenosine triphosphatePubChem0.935507.181
adenosine monophosphatePubChem0.922347.221
hydroxyl radicalsPubChem0.90217.0073
H(+)PubChem0.92.01588
pyrophosphatePubChem0.9177.975
HEPPSPubChem0.9252.331
protiumPubChem0.92.01576
deuteriumPubChem0.92.01588
Cpo-coa esterPubChem0.9971.713
CPD-9925PubChem0.9949.666
menadionePubChem0.85172.18
DB03059PubChem0.8851.607
DB01992PubChem0.8767.534
spirodilactonePubChem0.799204.179
vitamin K2PubChem0.764308.414