Receptor
PDB id Resolution Class Description Source Keywords
1N5J 1.85 Å EC: 2.7.4.9 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE DIPHOSPHATE (TDP) AND T HYMIDINE TRIPHOSPHATE (TTP) AT PH 5.4 (1.85 A RESOLUTION) MYCOBACTERIUM TUBERCULOSIS TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE) KINASE
Ref.: MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE: STRUCTURAL STUDIES OF INTERMEDIATES ALONG THE REACTION PATHWAY J.MOL.BIOL. V. 327 1077 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:217;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:215;
A:216;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
TTP A:219;
Valid;
none;
submit data
482.168 C10 H17 N2 O14 P3 CC1=C...
TYD A:218;
Valid;
none;
submit data
402.188 C10 H16 N2 O11 P2 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4UNR 1.98 Å EC: 2.7.4.9 MTB TMK IN COMPLEX WITH COMPOUND 23 MYCOBACTERIUM TUBERCULOSIS TRANSFERASE ATP TMP PHOSPHOTRANSFERASE
Ref.: STRUCTURE GUIDED LEAD GENERATION FOR M. TUBERCULOSI THYMIDYLATE KINASE (MTB TMK): DISCOVERY OF 3-CYANOP AND 1,6-NAPHTHYRIDIN-2-ONE AS POTENT INHIBITORS. J.MED.CHEM. V. 58 753 2015
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4UNP Kd = 590 uM TXW C12 H14 N2 O CCCc1cc2c(....
2 1N5I - TMP C10 H15 N2 O8 P CC1=CN(C(=....
3 1GSI - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1GTV - TMP C10 H15 N2 O8 P CC1=CN(C(=....
5 4UNS ic50 = 0.2 uM QZ3 C19 H18 N4 O3 S CCc1cc2c(c....
6 4UNR ic50 = 0.002 uM QZE C24 H16 N4 O3 c1cc(c2c(c....
7 4UNN ic50 = 0.42 uM QZZ C20 H14 N2 O4 COc1cccc(c....
8 1MRN Ki = 30 uM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
9 1W2G Ki = 27 uM THM C10 H14 N2 O5 CC1=CN(C(=....
10 1N5K - TMP C10 H15 N2 O8 P CC1=CN(C(=....
11 1N5L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
12 1W2H Ki ~ 10 uM ATM C10 H14 N5 O7 P CC1=CN(C(=....
13 1N5J - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
14 1MRS Ki = 110 uM 5HU C10 H15 N2 O9 P C1[C@@H]([....
15 4UNQ ic50 = 0.24 uM H6D C14 H9 F3 N2 O3 S C[S@@](=O)....
16 1G3U - TMP C10 H15 N2 O8 P CC1=CN(C(=....
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4UNP Kd = 590 uM TXW C12 H14 N2 O CCCc1cc2c(....
2 1N5I - TMP C10 H15 N2 O8 P CC1=CN(C(=....
3 1GSI - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1GTV - TMP C10 H15 N2 O8 P CC1=CN(C(=....
5 4UNS ic50 = 0.2 uM QZ3 C19 H18 N4 O3 S CCc1cc2c(c....
6 4UNR ic50 = 0.002 uM QZE C24 H16 N4 O3 c1cc(c2c(c....
7 4UNN ic50 = 0.42 uM QZZ C20 H14 N2 O4 COc1cccc(c....
8 1MRN Ki = 30 uM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
9 1W2G Ki = 27 uM THM C10 H14 N2 O5 CC1=CN(C(=....
10 1N5K - TMP C10 H15 N2 O8 P CC1=CN(C(=....
11 1N5L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
12 1W2H Ki ~ 10 uM ATM C10 H14 N5 O7 P CC1=CN(C(=....
13 1N5J - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
14 1MRS Ki = 110 uM 5HU C10 H15 N2 O9 P C1[C@@H]([....
15 4UNQ ic50 = 0.24 uM H6D C14 H9 F3 N2 O3 S C[S@@](=O)....
16 1G3U - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4UNP Kd = 590 uM TXW C12 H14 N2 O CCCc1cc2c(....
2 1N5I - TMP C10 H15 N2 O8 P CC1=CN(C(=....
3 1GSI - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1GTV - TMP C10 H15 N2 O8 P CC1=CN(C(=....
5 4UNS ic50 = 0.2 uM QZ3 C19 H18 N4 O3 S CCc1cc2c(c....
6 4UNR ic50 = 0.002 uM QZE C24 H16 N4 O3 c1cc(c2c(c....
7 4UNN ic50 = 0.42 uM QZZ C20 H14 N2 O4 COc1cccc(c....
8 1MRN Ki = 30 uM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
9 1W2G Ki = 27 uM THM C10 H14 N2 O5 CC1=CN(C(=....
10 1N5K - TMP C10 H15 N2 O8 P CC1=CN(C(=....
11 1N5L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
12 1W2H Ki ~ 10 uM ATM C10 H14 N5 O7 P CC1=CN(C(=....
13 1N5J - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
14 1MRS Ki = 110 uM 5HU C10 H15 N2 O9 P C1[C@@H]([....
15 4UNQ ic50 = 0.24 uM H6D C14 H9 F3 N2 O3 S C[S@@](=O)....
16 1G3U - TMP C10 H15 N2 O8 P CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TTP; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 TTP 1 1
2 TYD 0.884058 1
3 TMP 0.760563 0.985714
4 TLO 0.722892 0.945205
5 DAU 0.701149 0.932432
6 TRH 0.689655 0.932432
7 1JB 0.689655 0.932432
8 18T 0.689655 0.932432
9 3R2 0.689655 0.92
10 TDX 0.689655 0.945205
11 T3Q 0.674157 0.907895
12 T3F 0.674157 0.907895
13 DWN 0.674157 0.907895
14 3YN 0.674157 0.932432
15 T46 0.666667 0.932432
16 0N2 0.666667 0.896104
17 MMF 0.659341 0.907895
18 0FX 0.659341 0.907895
19 QDM 0.645161 0.896104
20 FNF 0.638298 0.92
21 1YF 0.638298 0.92
22 JHZ 0.638298 0.884615
23 AKM 0.638298 0.886076
24 4TG 0.631579 0.92
25 D3T 0.62963 0.971831
26 TBD 0.62963 0.958904
27 DUT 0.62963 0.957143
28 T5A 0.61165 0.841463
29 LLT 0.605634 0.873239
30 THM 0.605634 0.873239
31 ATY 0.6 0.945205
32 QUH 0.588235 0.907895
33 FUH 0.588235 0.907895
34 AZD 0.586207 0.907895
35 UFP 0.56962 0.905405
36 0DN 0.567568 0.833333
37 DCP 0.55814 0.891892
38 5HU 0.54321 0.971831
39 BRU 0.54321 0.905405
40 DUD 0.542169 0.957143
41 DT DT DT DT DT 0.541667 0.945205
42 DT DT PST 0.540816 0.881579
43 5IU 0.536585 0.905405
44 FDM 0.536585 0.918919
45 NYM 0.536585 0.958333
46 ABT 0.531915 0.884615
47 T3P 0.531646 0.943662
48 THP 0.53012 0.971429
49 D4T 0.528736 0.928571
50 6U4 0.521277 0.848101
51 ATM 0.517241 0.894737
52 TQP 0.512605 0.864198
53 7SG 0.512605 0.864198
54 TXS 0.512195 0.789474
55 TPE 0.510204 0.894737
56 T4K 0.508333 0.853659
57 T5K 0.508333 0.853659
58 BVP 0.5 0.944444
59 T3S 0.5 0.789474
60 8DG 0.489583 0.829268
61 YYY 0.477273 0.891892
62 2DT 0.47561 0.957747
63 DT DT DT 0.473118 0.878378
64 4TA 0.469565 0.807229
65 DT ME6 DT 0.468468 0.87013
66 D4D 0.449438 0.928571
67 DU 0.447059 0.942857
68 UMP 0.447059 0.942857
69 AZZ 0.447059 0.779221
70 DUP 0.430108 0.930556
71 UTP 0.428571 0.875
72 8DD 0.424242 0.8125
73 WMJ 0.42 0.761905
74 DDN 0.418605 0.942857
75 8GD 0.418367 0.829268
76 DGT 0.415842 0.759036
77 UC5 0.406593 0.943662
78 ID2 0.402439 0.8
Ligand no: 2; Ligand: TYD; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 TYD 1 1
2 TTP 0.884058 1
3 TMP 0.80597 0.985714
4 TLO 0.716049 0.945205
5 DAU 0.694118 0.932432
6 18T 0.682353 0.932432
7 TDX 0.682353 0.945205
8 3R2 0.682353 0.92
9 1JB 0.682353 0.932432
10 TRH 0.682353 0.932432
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3F 0.666667 0.907895
15 T3Q 0.666667 0.907895
16 TBD 0.662338 0.958904
17 0N2 0.659091 0.896104
18 T46 0.659091 0.932432
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 LLT 0.641791 0.873239
23 THM 0.641791 0.873239
24 QDM 0.637363 0.896104
25 AKM 0.630435 0.886076
26 FNF 0.630435 0.92
27 JHZ 0.630435 0.884615
28 1YF 0.630435 0.92
29 4TG 0.623656 0.92
30 DUD 0.61039 0.957143
31 0DN 0.6 0.833333
32 UFP 0.6 0.905405
33 DT DT DT DT DT 0.582418 0.945205
34 QUH 0.58 0.907895
35 FUH 0.58 0.907895
36 T5A 0.572816 0.841463
37 5HU 0.571429 0.971831
38 BRU 0.571429 0.905405
39 FDM 0.564103 0.918919
40 NYM 0.564103 0.958333
41 5IU 0.564103 0.905405
42 DT DT PST 0.56383 0.881579
43 T3P 0.56 0.943662
44 THP 0.556962 0.971429
45 ATM 0.542169 0.894737
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 TXS 0.538462 0.789474
49 YYY 0.536585 0.891892
50 T3S 0.525 0.789474
51 BVP 0.52381 0.944444
52 ABT 0.521739 0.884615
53 DT DT DT 0.511364 0.878378
54 D4D 0.506024 0.928571
55 7SG 0.504274 0.864198
56 TQP 0.504274 0.864198
57 T5K 0.5 0.853659
58 TPE 0.5 0.894737
59 DT ME6 DT 0.5 0.87013
60 T4K 0.5 0.853659
61 2DT 0.5 0.957747
62 4TA 0.486486 0.807229
63 DCP 0.477273 0.891892
64 8DD 0.473118 0.8125
65 AZZ 0.469136 0.779221
66 UMP 0.469136 0.942857
67 DU 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 D4T 0.449438 0.928571
71 DUP 0.449438 0.930556
72 6U4 0.447917 0.848101
73 DDN 0.439024 0.942857
74 3DT 0.428571 0.835616
75 UC5 0.425287 0.943662
76 ID2 0.423077 0.8
77 DT MA7 DT 0.420635 0.797619
78 8DG 0.418367 0.829268
79 DUN 0.41573 0.930556
80 DUT MG 0.413043 0.864865
81 5GW 0.410526 0.878378
82 DC 0.406977 0.878378
83 DCM 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 ADS THS THS THS 0.403361 0.767442
86 74W 0.4 0.732558
87 D4M 0.4 0.914286
88 74X 0.4 0.732558
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UNR; Ligand: QZE; Similar sites found: 2
This union binding pocket(no: 1) in the query (biounit: 4unr.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1E2K TMC 0.008551 0.40619 4.7619
2 5LX9 OLA 0.00168 0.4444 6.66667
Pocket No.: 2; Query (leader) PDB : 4UNR; Ligand: QZE; Similar sites found: 11
This union binding pocket(no: 2) in the query (biounit: 4unr.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ALG HP6 0.009732 0.40435 None
2 2ALG DAO 0.009732 0.40435 None
3 4OIV XX9 0.02994 0.40124 1.42857
4 1R5L VIV 0.005014 0.42248 2.85714
5 3V66 D3A 0.02031 0.41045 3.33333
6 3WCA FPS 0.01639 0.4001 3.80952
7 4H07 IPH 0.01792 0.40226 3.8961
8 5A4W QCT 0.03176 0.40267 4.28571
9 3D5Z FUB AHR AHR 0.001358 0.43923 6.19048
10 5LWY OLA 0.004101 0.41767 6.66667
11 5C2H 4PX 0.01821 0.41085 22.381
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