SInCRe - Rv3307

Tuberculist information

Gene name	deoD
Protein function	Probable purine nucleoside phosphorylase DeoD (inosine phosphorylase) (PNP)
Functional category(tuberculist)	intermediary metabolism and respiration
Gene location(kb)	3694.05
Molecular mass(da)	27539.5
External sites	TB Database TubercuList WebTB

Protein sequence

Number of amino acids : 268

	  		  	1    VADPRPDPDELARRAAQVIADRTGIGEHDVAVVLGSGWLPAVAALGSPTTVLPQAELPGF   60
			  	61   VPPTAAGHAGELLSVPIGAHRVLVLAGRIHAYEGHDLRYVVHPVRAARAAGAQIMVLTNA  120
			  	121  AGGLRADLQVGQPVLISDHLNLTARSPLVGGEFVDLTDAYSPRLRELARQSDPQLAEGVY  180
			  	181  AGLPGPHYETPAEIRMLQTLGADLVGMSTVHETIAARAAGAEVLGVSLVTNLAAGITGEP  240
			  	241  LSHAEVLAAGAASATRMGALLADVIARF

Known structures in the PDB

	PDB ID	1G2O
	Total residue count	804
	Number of chains	3
	Method	X-RAY
	Resolution	1.75

	PDB ID	1I80
	Total residue count	804
	Number of chains	3
	Method	X-RAY
	Resolution	2

	PDB ID	1N3I
	Total residue count	804
	Number of chains	3
	Method	X-RAY
	Resolution	1.9

	PDB ID	3IOM
	Total residue count	536
	Number of chains	2
	Method	X-RAY
	Resolution	2.14

	PDB ID	3SCZ
	Total residue count	536
	Number of chains	2
	Method	X-RAY
	Resolution	1.95

Number of amino acids : 268

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
PNP_UDP_1	PF01048	29-266

Mtb Structural Proteome models

Model Number	1
Model name	Rv3307_1g2o_A
Template	1G2O APDB CREDO
Template coverage	7_268
Template Identity(%)	100.0
Model coverage(%)	97.4
Normalized DOPE score	-1.656

Model Number	2
Model name	Rv3307
Template	1G2O APDB CREDO
Template coverage	7_268
Template Identity(%)	100.0
Model coverage(%)	97.4
Normalized DOPE score	-1.401

Structure Models from Chopin

Model Number	1
Profile	c.56.2.1 - 3.40.50.1580 Click for model details
zscore	29.17
Residue begin	1
Residue end	268

Binding pockets

STRING

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

Protein interacting with Rv3307	Gene name	Confidence Score
Rv3313c	add	0.996
Rv3315c	cdd	0.989
Rv2202c	adoK	0.982
Rv2584c	apt	0.974
Rv3624c	hpt	0.973
Rv3393	iunH	0.964
Rv3314c	deoA	0.941
Rv3314c	deoA	0.941
Rv3314c	deoA	0.941
Rv0573c	pncB2	0.939
Rv3309c	upp	0.931
Rv2043c	pncA	0.929
Rv1330c	pncB1	0.912
Rv3308	pmmB	0.911
Rv3308	pmmB	0.911
Rv3308	pmmB	0.911
Rv3308	pmmB	0.911
Rv1379	pyrR	0.903
Rv2344c	dgt	0.903
Rv2344c	dgt	0.903
Rv0478	deoC	0.902

Potential ligand/drug binding sites

Protein Model	Pocket Number	Drug Binding Site	PMIN Score	Pvalue PMIN	PMAX Score	Pvalue PMAX
Rv3307_1g2o_A	1	3f8w_ADN_A_300 PDB CREDO	0.757	0.044	0.656	0.001
Rv3307_1g2o_A	1	3f8w_ADN_B_301 PDB CREDO	0.755	0.045	0.654	0.001
Rv3307_1g2o_A	1	3f8w_ADN_C_302 PDB CREDO	0.745	0.051	0.646	0.001
Rv3307_1g2o_A	1	3mdv_CL6_B_506 PDB CREDO	0.605	0.173	0.605	0.002
Rv3307_1g2o_A	1	2eva_ADN_A_498 PDB CREDO	0.578	0.206	0.578	0.003
Rv3307_1g2o_A	3	1pg2_ADN_A_552 PDB CREDO	0.653	0.122	0.564	0.004
Rv3307_1g2o_A	1	3mdv_CL6_A_506 PDB CREDO	0.650	0.124	0.563	0.004
Rv3307_1g2o_A	1	2jap_J01_D_1249 PDB CREDO	0.587	0.195	0.559	0.004
Rv3307_1g2o_A	3	2y7j_B49_A_1294 PDB CREDO	0.677	0.100	0.558	0.004
Rv3307_1g2o_A	1	2jap_J01_B_1249 PDB CREDO	0.583	0.200	0.555	0.005
Rv3307_1g2o_A	1	1qhs_CLM_A_999 PDB CREDO	0.554	0.239	0.554	0.005
Rv3307_1g2o_A	1	2jap_J01_A_1249 PDB CREDO	0.580	0.203	0.553	0.005
Rv3307_1g2o_A	1	2jap_J01_C_1249 PDB CREDO	0.578	0.206	0.551	0.005
Rv3307_1g2o_A	1	2bxf_DZP_A_2001 PDB CREDO	0.627	0.148	0.543	0.006
Rv3307_1g2o_A	1	2bxf_DZP_B_2001 PDB CREDO	0.626	0.150	0.542	0.006
Rv3307_1g2o_A	1	2nnj_225_A_501 PDB CREDO	0.540	0.258	0.540	0.006
Rv3307_1g2o_A	3	2y7j_B49_C_1294 PDB CREDO	0.567	0.221	0.539	0.006
Rv3307_1g2o_A	1	3uq6_ADN_B_401 PDB CREDO	0.590	0.191	0.536	0.006
Rv3307_1g2o_A	1	3hbb_TMQ_B_612 PDB CREDO	0.535	0.265	0.535	0.006
Rv3307_1g2o_A	1	2w9s_TOP_E_1160 PDB CREDO	0.562	0.228	0.534	0.006
Rv3307_1g2o_A	1	1e7a_PFL_A_4001 PDB CREDO	0.622	0.154	0.533	0.007
Rv3307_1g2o_A	2	1lin_TFP_A_154 PDB CREDO	0.568	0.220	0.531	0.007
Rv3307_1g2o_A	1	2bxe_1FL_A_2001 PDB CREDO	0.556	0.236	0.530	0.007
Rv3307_1g2o_A	1	3mdt_VOR_A_506 PDB CREDO	0.617	0.159	0.529	0.007
Rv3307_1g2o_A	1	2bxe_1FL_B_2001 PDB CREDO	0.555	0.237	0.528	0.007
Rv3307_1g2o_A	1	1e7a_PFL_B_4001 PDB CREDO	0.616	0.160	0.528	0.007
Rv3307_1g2o_A	1	2bdm_TMI_A_502 PDB CREDO	0.528	0.276	0.528	0.007
Rv3307_1g2o_A	1	3ay0_ADN_A_401 PDB CREDO	0.528	0.276	0.528	0.007
Rv3307_1g2o_A	1	3ilt_TRU_E_800 PDB CREDO	0.528	0.276	0.528	0.007
Rv3307_1g2o_A	1	3jw5_TOP_B_208 PDB CREDO	0.584	0.198	0.528	0.007
Rv3307_1g2o_A	1	3ay0_ADN_B_402 PDB CREDO	0.527	0.277	0.527	0.007
Rv3307_1g2o_A	1	3jw5_TOP_A_208 PDB CREDO	0.583	0.200	0.527	0.007
Rv3307_1g2o_A	1	3uq6_ADN_A_401 PDB CREDO	0.579	0.205	0.526	0.007
Rv3307_1g2o_A	3	1gwr_EST_A_600 PDB CREDO	0.637	0.137	0.525	0.007
Rv3307_1g2o_A	3	2y7j_B49_D_1294 PDB CREDO	0.667	0.109	0.525	0.007
Rv3307_1g2o_A	1	1v3q_2DI_E_290 PDB CREDO	0.867	0.007	0.524	0.008
Rv3307_1g2o_A	1	3ik6_HCZ_B_800 PDB CREDO	0.551	0.242	0.524	0.008
Rv3307_1g2o_A	1	1iol_EST_A_400 PDB CREDO	0.577	0.208	0.524	0.008
Rv3307_1g2o_A	3	1gwr_EST_B_600 PDB CREDO	0.635	0.140	0.523	0.008
Rv3307_1g2o_A	1	2w9h_TOP_A_1160 PDB CREDO	0.602	0.176	0.522	0.008
Rv3307_1g2o_A	3	1pcg_EST_B_2 PDB CREDO	0.633	0.141	0.522	0.008
Rv3307_1g2o_A	3	1uay_ADN_A_1001 PDB CREDO	0.632	0.143	0.521	0.008
Rv3307_1g2o_A	3	3rem_SAL_A_301 PDB CREDO	0.521	0.287	0.521	0.008
Rv3307_1g2o_A	3	3rem_SAL_B_301 PDB CREDO	0.521	0.287	0.521	0.008
Rv3307_1g2o_A	3	1ere_EST_B_600 PDB CREDO	0.631	0.144	0.520	0.008
Rv3307_1g2o_A	1	2ydo_ADN_A_400 PDB CREDO	0.655	0.120	0.519	0.008
Rv3307_1g2o_A	3	1ere_EST_A_600 PDB CREDO	0.628	0.147	0.518	0.008
Rv3307_1g2o_A	3	1ere_EST_E_600 PDB CREDO	0.628	0.147	0.518	0.008
Rv3307_1g2o_A	1	3clb_TMQ_D_614 PDB CREDO	0.570	0.217	0.517	0.008
Rv3307_1g2o_A	1	3hbb_TMQ_D_614 PDB CREDO	0.570	0.217	0.517	0.008
Rv3307_1g2o_A	1	1udu_CIA_A_1003 PDB CREDO	0.543	0.254	0.517	0.008
Rv3307_1g2o_A	1	3mdt_VOR_B_506 PDB CREDO	0.602	0.177	0.516	0.009
Rv3307_1g2o_A	1	3n8w_FLP_A_701 PDB CREDO	0.516	0.294	0.516	0.009
Rv3307_1g2o_A	1	3fl9_TOP_A_200 PDB CREDO	0.568	0.219	0.513	0.009
Rv3307_1g2o_A	3	1qku_EST_B_600 PDB CREDO	0.622	0.154	0.513	0.009
Rv3307_1g2o_A	1	3ijx_HCZ_B_800 PDB CREDO	0.538	0.260	0.512	0.009
Rv3307_1g2o_A	3	1qku_EST_C_600 PDB CREDO	0.621	0.155	0.512	0.009
Rv3307_1g2o_A	3	1qku_EST_A_600 PDB CREDO	0.618	0.158	0.510	0.009
Rv3307_1g2o_A	3	1yi4_ADN_A_306 PDB CREDO	0.565	0.224	0.509	0.009
Rv3307_1g2o_A	3	1g50_EST_B_1600 PDB CREDO	0.617	0.160	0.508	0.010
Rv3307_1g2o_A	1	3hbb_TMQ_A_611 PDB CREDO	0.560	0.231	0.508	0.010
Rv3307_1g2o_A	1	3fl9_TOP_C_200 PDB CREDO	0.592	0.189	0.507	0.010
Rv3307_1g2o_A	1	3ik6_HCZ_B_262 PDB CREDO	0.561	0.228	0.507	0.010
Rv3307_1g2o_A	1	1fdw_EST_A_350 PDB CREDO	0.623	0.152	0.506	0.010
Rv3307_1g2o_A	3	3ug2_IRE_A_1 PDB CREDO	0.532	0.270	0.506	0.010
Rv3307_1g2o_A	1	1qhy_CLM_A_999 PDB CREDO	0.505	0.311	0.505	0.010
Rv3307_1g2o_A	1	3tbg_RTZ_D_1 PDB CREDO	0.529	0.274	0.504	0.010
Rv3307_1g2o_A	1	3fl9_TOP_G_200 PDB CREDO	0.557	0.234	0.504	0.010
Rv3307_1g2o_A	1	3qfx_CP6_A_602 PDB CREDO	0.620	0.156	0.504	0.010
Rv3307_1g2o_A	1	3tq8_TOP_A_2001 PDB CREDO	0.557	0.234	0.504	0.010
Rv3307_1g2o_A	1	2x7h_PFN_A_1372 PDB CREDO	0.554	0.239	0.503	0.010
Rv3307_1g2o_A	1	3tbg_RTZ_B_1 PDB CREDO	0.554	0.239	0.503	0.010
Rv3307_1g2o_A	1	1mrl_DOL_C_302 PDB CREDO	0.502	0.315	0.502	0.011
Rv3307_1g2o_A	1	3qfx_CP6_B_702 PDB CREDO	0.619	0.157	0.502	0.011
Rv3307_1g2o_A	1	3clb_TMQ_C_613 PDB CREDO	0.552	0.241	0.502	0.011
Rv3307_1g2o_A	1	2w9s_TOP_C_1160 PDB CREDO	0.555	0.237	0.501	0.011
Rv3307_1g2o_A	1	3fl9_TOP_B_200 PDB CREDO	0.555	0.237	0.501	0.011
Rv3307_1g2o_A	1	3mg0_BO2_Y_1403 PDB CREDO	0.585	0.198	0.501	0.011

Similarity to known drug target from sensitive sequence analysis

No drug targets

List of small molecules tested from TIBLE

View results in TIBLE page

Name	Affinity	Assay description	DOI
CHEMBL1172777	pKd = 3.5 None	Binding affinity to Mycobacterium tuberculosis purine nucleoside phosphorylase by spectrophotometric analysis	http://www.ncbi.nlm.nih.gov/pubmed/20570524
CHEMBL1425	pKd = 4.1 None	Binding affinity to Mycobacterium tuberculosis purine nucleoside phosphorylase by spectrophotometric analysis	http://www.ncbi.nlm.nih.gov/pubmed/20570524
CHEMBL1467	pKd = 3 None	Binding affinity to Mycobacterium tuberculosis purine nucleoside phosphorylase by spectrophotometric analysis	http://www.ncbi.nlm.nih.gov/pubmed/20570524
CHEMBL182	pKd = 4.8 None	Binding affinity to Mycobacterium tuberculosis purine nucleoside phosphorylase by spectrophotometric analysis	http://www.ncbi.nlm.nih.gov/pubmed/20570524
CHEMBL184	pKd = 4.9 None	Binding affinity to Mycobacterium tuberculosis purine nucleoside phosphorylase by spectrophotometric analysis	http://www.ncbi.nlm.nih.gov/pubmed/20570524
CHEMBL266540	pKd = 3.5 None	Binding affinity to Mycobacterium tuberculosis purine nucleoside phosphorylase by spectrophotometric analysis	http://www.ncbi.nlm.nih.gov/pubmed/20570524
CHEMBL388931	pKd = 4.9 None	Binding affinity to Mycobacterium tuberculosis purine nucleoside phosphorylase by spectrophotometric analysis	http://www.ncbi.nlm.nih.gov/pubmed/20570524
CHEMBL859	pKd = 3.1 None	Binding affinity to Mycobacterium tuberculosis purine nucleoside phosphorylase by spectrophotometric analysis	http://www.ncbi.nlm.nih.gov/pubmed/20570524

Off-target activity - ligand based from TIBLE

View results in TIBLE page

Predicted off-target	Method	Summary	Full results
Glutathione S-transferase A1 1PL2	PharmMapper	3 hydroph + 3 HB + 2 pos/neg + 0 arom	Link
Glutathione S-transferase A1 1PL1	PharmMapper	3 hydroph + 6 HB + 2 pos/neg + 0 arom	Link
Adenosine kinase 1BX4	PharmMapper	0 hydroph + 8 HB + 0 pos/neg + 0 arom	Link
3-hydroxy-3-methylglutaryl-coenzyme A reductase 3CDA	PharmMapper	6 hydroph + 3 HB + 1 pos/neg + 0 arom	Link
Glucokinase 1V4S	PharmMapper	3 hydroph + 5 HB + 0 pos/neg + 0 arom	Link
Cyclic AMP phosphodiesterase	PASS	Pa = 0.743 & SM = CHEMBL605681	Link
Adenosine (A1) Agonist	SEA	E_value = 6.01e-62 & MaxTC = 0.56	Link
Purine Nucleoside Phosphorylase Inhibitor	SEA	E_value = 8.07e-58 & MaxTC = 0.55	Link
Adenosine A1 receptor	SEA	E_value = 8.52e-48 & MaxTC = 0.66	Link
phosphoglycerate kinase [-]	SEA	E_value = 8.46e-42 & MaxTC = 0.66	Link
Adenosine A3 receptor	SEA	E_value = 1.82e-39 & MaxTC = 0.66	Link
Adenosine A2b receptor	SEA	E_value = 2.51e-37 & MaxTC = 0.66	Link
Adenosine A2a receptor	SEA	E_value = 4.8e-35 & MaxTC = 0.66	Link
S-Adenosyl-L-Homocysteine Hydrolase Inhibitor	SEA	E_value = 1.03e-34 & MaxTC = 0.49	Link
Equilibrative nucleoside transporter 1	SEA	E_value = 8.81e-31 & MaxTC = 0.67	Link
adenosine kinase; adenosine 5-phosphotransferase	SEA	E_value = 9.89e-27 & MaxTC = 0.67	Link
Adenosylhomocysteinase	SEA	E_value = 1.47e-24 & MaxTC = 0.52	Link
rRNA [-]	SEA	E_value = 2.73e-24 & MaxTC = 0.6	Link
adenosine A2 receptor	SEA	E_value = 5.14e-24 & MaxTC = 0.66	Link
S-adenosyl-L-homocysteine hydrolase [-]	SEA	E_value = 7.34e-24 & MaxTC = 0.69	Link
P3 purinoceptor; P3 purinoceptor-like protein [-]	SEA	E_value = 2.32e-23 & MaxTC = 0.55	Link
glycosomal glyceraldehyde-3-phosphate dehydrogenase [-]	SEA	E_value = 2.14e-22 & MaxTC = 0.66	Link
Adenosine A3 receptor	SEA	E_value = 7.76e-22 & MaxTC = 0.65	Link
herpes simplex virus 2 thymidine kinase [-]	SEA	E_value = 6.87e-21 & MaxTC = 0.65	Link
ATP-dependent RNA helicase [-]	SEA	E_value = 7.92e-20 & MaxTC = 0.53	Link
Hypoxanthine-guanine phosphoribosyltransferase	SEA	E_value = 4.38e-19 & MaxTC = 0.57	Link
Adenosine A1 receptor	SEA	E_value = 1.46e-17 & MaxTC = 0.63	Link
adenosine A1 receptor [-]	SEA	E_value = 5.93e-16 & MaxTC = 0.66	Link
P2Y purinoceptor [-]	SEA	E_value = 6.65e-16 & MaxTC = 0.66	Link
adenosine A2 receptor [+]	SEA	E_value = 7.31e-15 & MaxTC = 0.66	Link
P2Y purinoceptor	SEA	E_value = 1.54e-14 & MaxTC = 0.66	Link
Adenosine kinase	SEA	E_value = 1.64e-14 & MaxTC = 0.66	Link
adenosine A2A receptor [-]	SEA	E_value = 5.37e-14 & MaxTC = 0.66	Link
nonstructural protein NS5B; RNA-directed RNA polymerase [-]	SEA	E_value = 5.52e-14 & MaxTC = 0.47	Link
Adenosylhomocysteinase	SEA	E_value = 9.86e-14 & MaxTC = 0.56	Link
adenosine A2B receptor	SEA	E_value = 1.82e-13 & MaxTC = 0.46	Link
glycosomal glyceraldehyde-3-phosphate dehydrogenase	SEA	E_value = 3.63e-13 & MaxTC = 0.44	Link
P2Y purinoceptor 1 [+]	SEA	E_value = 3.63e-13 & MaxTC = 0.51	Link
adenosine A3 receptor	SEA	E_value = 7.27e-13 & MaxTC = 0.56	Link
GTPase HRas precursor; transforming protein p21; p21ras; H-Ras-1; c-H-ras [-]	SEA	E_value = 9.09e-13 & MaxTC = 0.7	Link
putrescine aminopropyltransferase; spermidine synthase [-]	SEA	E_value = 3.27e-12 & MaxTC = 0.48	Link
West Nile virus NTPase/helicase [-]	SEA	E_value = 4.54e-12 & MaxTC = 0.44	Link
2-5A-dependent ribonuclease; ribonuclease L	SEA	E_value = 6.18e-12 & MaxTC = 0.43	Link
P2Y12 platelet ADP receptor; P2YC purinoceptor 12 [-]	SEA	E_value = 1.98e-11 & MaxTC = 0.45	Link

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	0.998	96.9872
forodesinePubChem	0.996	266.253
DB03551PubChem	0.993	267.304
inosinePubChem	0.993	268.226
guaninePubChem	0.992	151.126
guanosinePubChem	0.991	283.241
9-deazahypoxanthinePubChem	0.987	135.123
1,4-dideoxy-1,4-imino-D-arabinitolPubChem	0.986	133.146
hypoxanthinePubChem	0.981	136.111
SODIUM XANTHINEPubChem	0.979	152.111
hydron diphosphatePubChem	0.978	391.981
ribose 1-phosphatePubChem	0.972	230.11
adenosinePubChem	0.972	267.241
purine nucleosidePubChem	0.969	252.227
7-[[(3R,4R)-3-hydroxy-4-methylol-pyrrolidino]methyl]-3,4a,5,7a-tetrahydropyrrolo[3,2-d]pyrimidin-4-oPubChem	0.968	267.304
deoxyinosinePubChem	0.967	252.227
deoxyguanosinePubChem	0.965	267.241
nicotinamide ribosidePubChem	0.962	255.247
purine basePubChem	0.961	120.112
adeninePubChem	0.958	135.127
deoxyadenosinePubChem	0.949	251.242
nicotinic acidPubChem	0.941	122.101
1,4-dideoxy-1,4-imino-D-ribitolPubChem	0.94	133.146
deoxyuridinePubChem	0.927	228.202
ribose 1PPubChem	0.927	230.11
uracilPubChem	0.917	112.087
vitamin BPubChem	0.915	122.125
deoxyribose-1-phosphatePubChem	0.91	214.11
nicotinamide ribosePubChem	0.9	255.247
sulfatePubChem	0.894	96.0626
didanosinePubChem	0.841	236.227
9-(5',5'-difluoro-5'-phosphonopentyl)guaninePubChem	0.839	337.22
8-aminoguanosinePubChem	0.834	298.255
BCX-34PubChem	0.829	241.249
8-amino-9-(2-thienylmethyl)guaninePubChem	0.826	262.291
8-aminoguaninePubChem	0.815	166.141
Immucillin-GPubChem	0.803	281.268
1,4-dideoxy-1,4-imino-L-arabinitolPubChem	0.8	133.146
DB03743PubChem	0.8	266.253
2-amino-6-mercapto-7-methylpurine ribonucleosidePubChem	0.796	313.333
MDL 74,428PubChem	0.789	347.266
hydron sulfatePubChem	0.782	196.157
vanadatePubChem	0.768	98.9397
magnesiumPubChem	0.764	24.305
8-azaguaninePubChem	0.754	152.114
8-amino-9-benzylguaninePubChem	0.751	256.263
manganesePubChem	0.741	54.938
9-deaza-9-(3-thienylmethyl)guaninePubChem	0.737	246.288
CI-972PubChem	0.714	297.764
CHEBI:228007PubChem	0.711	240.261