SInCRe - Rv2445c

Tuberculist information

Gene name	ndkA
Protein function	Probable nucleoside diphosphate kinase NdkA (NDK) (NDP kinase) (nucleoside-2-P kinase)
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	2745.31
Molecular mass(da)	14475.5
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 136

	  		  	1    VTERTLVLIKPDGIERQLIGEIISRIERKGLTIAALQLRTVSAELASQHYAEHEGKPFFG   60
			  	61   SLLEFITSGPVVAAIVEGTRAIAAVRQLAGGTDPVQAAAPGTIRGDFALETQFNLVHGSD  120
			  	121  SAESAQREIALWFPGA

Known structures in the PDB

	PDB ID	1K44
	Total residue count	816
	Number of chains	6
	Method	X-RAY
	Resolution	2.6

	PDB ID	4ANC
	Total residue count	136
	Number of chains	1
	Method	X-RAY
	Resolution	2.8

	PDB ID	4AND
	Total residue count	272
	Number of chains	2
	Method	X-RAY
	Resolution	2.81

	PDB ID	4ANE
	Total residue count	816
	Number of chains	6
	Method	X-RAY
	Resolution	1.9

Number of amino acids : 136

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
NDK	PF00334	3-136

Mtb Structural Proteome models

Model Number	1
Model name	Rv2445c_1k44_A
Template	1K44 APDB CREDO
Template coverage	2_136
Template Identity(%)	100.0
Model coverage(%)	98.5
Normalized DOPE score	-1.711

Model Number	2
Model name	Rv2445c
Template	1K44 APDB CREDO
Template coverage	2_136
Template Identity(%)	100.0
Model coverage(%)	98.5
Normalized DOPE score	-1.49

Structure Models from Chopin

Model Number	1
Profile	d.58.6.1 - 3.30.70.141 Click for model details
zscore	39.63
Residue begin	1
Residue end	136

Binding pockets

STRING

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

Protein interacting with Rv2445c	Gene name	Confidence Score
Rv0733	adk	0.995
Rv1617	pykA	0.991
Rv1699	pyrG	0.991
Rv1699	pyrG	0.991
Rv1617	pykA	0.991
Rv2697c	dut	0.989
Rv2883c	pyrH	0.988
Rv2783c	gpsI	0.987
Rv2783c	gpsI	0.987
Rv2783c	gpsI	0.987
Rv2783c	gpsI	0.987
Rv2783c	gpsI	0.987
Rv3247c	tmk	0.986
Rv3721c	dnaZX	0.986
Rv3721c	dnaZX	0.986
Rv1712	cmk	0.984
Rv1341	Rv1341	0.983
Rv3457c	rpoA	0.982
Rv3457c	rpoA	0.982
Rv3457c	rpoA	0.982
Rv1389	gmk	0.981
Rv3051c	nrdE	0.98
Rv3051c	nrdE	0.98
Rv3051c	nrdE	0.98
Rv3609c	folE	0.978
Rv0321	dcd	0.978
Rv0667	rpoB	0.975
Rv0667	rpoB	0.975
Rv0667	rpoB	0.975
Rv0667	rpoB	0.975
Rv0667	rpoB	0.975
Rv0667	rpoB	0.975
Rv0952	sucD	0.973
Rv0952	sucD	0.973
Rv0570	nrdZ	0.967
Rv0570	nrdZ	0.967
Rv0570	nrdZ	0.967
Rv0668	rpoC	0.966
Rv0668	rpoC	0.966
Rv0668	rpoC	0.966
Rv0668	rpoC	0.966
Rv0668	rpoC	0.966
Rv1438	tpi	0.965
Rv0002	dnaN	0.955
Rv0002	dnaN	0.955
Rv0002	dnaN	0.955
Rv2583c	relA	0.954
Rv2583c	relA	0.954
Rv2583c	relA	0.954
Rv2583c	relA	0.954
Rv2580c	hisS	0.953
Rv2580c	hisS	0.953
Rv3048c	nrdF2	0.95
Rv2448c	valS	0.949
Rv2448c	valS	0.949
Rv2448c	valS	0.949
Rv0951	sucC	0.943
Rv0951	sucC	0.943
Rv1021	Rv1021	0.942
Rv2976c	ung	0.941
Rv2447c	folC	0.939
Rv2447c	folC	0.939
Rv3356c	folD	0.939
Rv3356c	folD	0.939
Rv1981c	nrdF1	0.937
Rv1023	eno	0.933
Rv1023	eno	0.933
Rv2984	ppk1	0.932
Rv2984	ppk1	0.932
Rv2984	ppk1	0.932
Rv1547	dnaE1	0.93
Rv1547	dnaE1	0.93
Rv1547	dnaE1	0.93
Rv1547	dnaE1	0.93
Rv2344c	dgt	0.929
Rv2344c	dgt	0.929
Rv3628	ppa	0.924
Rv1629	polA	0.92
Rv2192c	trpD	0.92
Rv1629	polA	0.92
Rv2192c	trpD	0.92
Rv1629	polA	0.92
Rv1392	metK	0.919
Rv1392	metK	0.919
Rv1392	metK	0.919
Rv0013	trpG	0.918
Rv2995c	leuB	0.916
Rv3711c	dnaQ	0.916
Rv0721	rpsE	0.913
Rv0721	rpsE	0.913
Rv2540c	aroF	0.913
Rv3309c	upp	0.912
Rv1380	pyrB	0.911
Rv1380	pyrB	0.911
Rv1408	rpe	0.909
Rv2413c	Rv2413c	0.906
Rv2462c	tig	0.905
Rv2462c	tig	0.905
Rv2462c	tig	0.905
Rv1437	pgk	0.903

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

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
phosphatePubChem	0.993	96.9872
guanosine diphosphatePubChem	0.988	443.201
adenosine diphosphatePubChem	0.98	427.201
cytidine diphosphatePubChem	0.978	403.176
adenosine triphosphatePubChem	0.971	507.181
pyrophosphatePubChem	0.963	177.975
guanosine triphosphatePubChem	0.952	523.18
thymidine diphosphatePubChem	0.945	402.188
dUMPPubChem	0.945	308.182
thymidylatePubChem	0.943	322.208
dGDPPubChem	0.942	427.201
pppGppPubChem	0.94	683.14
guanosine tetraphosphatePubChem	0.938	603.16
uridine diphosphatePubChem	0.938	404.161
dADPPubChem	0.928	411.202
guanylatePubChem	0.918	363.221
polyglutaminePubChem	0.915	146.145
deoxyguanosine triphosphatePubChem	0.911	507.181
deuteriumPubChem	0.901	2.01588
H(+)PubChem	0.901	2.01588
dUDPPubChem	0.9	388.162
adenosine monophosphatePubChem	0.9	347.221
protiumPubChem	0.9	2.01576
thymidine triphosphatePubChem	0.9	482.168
deoxyuridine triphosphatePubChem	0.9	468.142
YYYPubChem	0.9	387.177
polyuridylic acidPubChem	0.9	324.181
glutaminPubChem	0.9	146.145
poly CPubChem	0.9	323.197
cytidine triphosphatePubChem	0.9	483.156
dITPPubChem	0.9	492.166
ammoniaPubChem	0.9	17.0305
glutamatePubChem	0.9	147.129
inosine triphosphatePubChem	0.9	508.166
deoxyadenosine triphosphatePubChem	0.9	491.182
hydroxyl radicalsPubChem	0.9	17.0073
deoxycytidine triphosphatePubChem	0.9	467.157
uridine triphosphatePubChem	0.9	484.141
ara-CTPPubChem	0.9	483.156
magnesiumPubChem	0.88	24.305
calciumPubChem	0.824	40.078
polyethylene glycolPubChem	0.816	62.0678
Tween 20PubChem	0.815	522.669
sulfatePubChem	0.806	96.0626
NDPSPubChem	0.8	244.074
hydron sulfatePubChem	0.794	196.157
Tris-HClPubChem	0.769	121.135
hydron diphosphatePubChem	0.748	391.981
ethylene glycol; hydronPubChem	0.745	63.0758
cyclic AMPPubChem	0.744	329.206
selenomethioninePubChem	0.73	196.106
SeMetPubChem	0.73	196.106
[gamma-32P]GTPPubChem	0.723	524.181
Gpp(NH)pPubChem	0.712	522.196
chloridePubChem	0.712	35.453
AMPPNPPubChem	0.712	506.196