Receptor
PDB id Resolution Class Description Source Keywords
2B8T 2 Å EC: 2.7.1.21 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM U.UREALYTICUM IN COMPLEX WITH THYMIDINE UREAPLASMA PARVUM DEOXYRIBONUCLEOSIDE KINASE ZINC-BINDING DOMAIN TK1 UU-TKTHYMIDINE TRANSFERASE
Ref.: STRUCTURE OF THE SUBSTRATE COMPLEX OF THYMIDINE KINASE FROM UREAPLASMA UREALYTICUM AND INVESTIGATIONS OF POSSIBLE DRUG TARGETS FOR THE ENZYME FEBS LETT. V. 272 6365 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
THM A:4970;
B:5970;
C:6970;
D:7970;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
242.229 C10 H14 N2 O5 CC1=C...
TRS D:5006;
Invalid;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
ZN A:1218;
B:2218;
C:3218;
D:4218;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2B8T 2 Å EC: 2.7.1.21 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM U.UREALYTICUM IN COMPLEX WITH THYMIDINE UREAPLASMA PARVUM DEOXYRIBONUCLEOSIDE KINASE ZINC-BINDING DOMAIN TK1 UU-TKTHYMIDINE TRANSFERASE
Ref.: STRUCTURE OF THE SUBSTRATE COMPLEX OF THYMIDINE KINASE FROM UREAPLASMA UREALYTICUM AND INVESTIGATIONS OF POSSIBLE DRUG TARGETS FOR THE ENZYME FEBS LETT. V. 272 6365 2005
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2B8T - THM C10 H14 N2 O5 CC1=CN(C(=....
2 2UZ3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2B8T - THM C10 H14 N2 O5 CC1=CN(C(=....
2 2UZ3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2B8T - THM C10 H14 N2 O5 CC1=CN(C(=....
2 2UZ3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: THM; Similar ligands found: 73
No: Ligand ECFP6 Tc MDL keys Tc
1 THM 1 1
2 LLT 1 1
3 0DN 0.777778 0.923077
4 TXS 0.704918 0.869565
5 TMP 0.693548 0.859155
6 T3S 0.68254 0.869565
7 TYD 0.641791 0.873239
8 ID2 0.637931 0.910448
9 T3P 0.629032 0.84507
10 TBD 0.623188 0.837838
11 AZZ 0.609375 0.857143
12 TTP 0.605634 0.873239
13 BVD 0.587302 0.953846
14 BTD 0.550725 0.873239
15 3DT 0.540984 0.953846
16 FDM 0.536232 0.8
17 NYM 0.536232 0.835616
18 THP 0.528571 0.84507
19 WMJ 0.525 0.78481
20 DAU 0.52381 0.863014
21 TLO 0.518519 0.849315
22 ATM 0.513514 0.779221
23 DUR 0.508197 0.952381
24 0TT 0.506494 0.926471
25 DT DT DT 0.5 0.833333
26 3YN 0.5 0.837838
27 3R2 0.494118 0.826667
28 TDX 0.494118 0.849315
29 18T 0.494118 0.837838
30 1JB 0.494118 0.837838
31 TRH 0.494118 0.837838
32 MCY 0.492308 0.925373
33 74W 0.488636 0.775
34 74X 0.488636 0.775
35 DT DT DT DT DT 0.488372 0.824324
36 ATY 0.487179 0.824324
37 T3F 0.482759 0.815789
38 T3Q 0.482759 0.815789
39 DWN 0.482759 0.815789
40 5HU 0.478873 0.873239
41 T46 0.477273 0.837838
42 0N2 0.477273 0.805195
43 AZD 0.475 0.792208
44 DT DT PST 0.47191 0.813333
45 MMF 0.47191 0.815789
46 0FX 0.47191 0.815789
47 UFP 0.464789 0.786667
48 2DT 0.463768 0.833333
49 QDM 0.461538 0.805195
50 BRU 0.458333 0.786667
51 AKM 0.456522 0.775
52 FNF 0.456522 0.826667
53 1YF 0.456522 0.826667
54 JHZ 0.456522 0.794872
55 5IU 0.452055 0.786667
56 4TG 0.451613 0.826667
57 BVP 0.435897 0.821918
58 T5A 0.431373 0.756098
59 TMC 0.426471 0.882353
60 ABT 0.425287 0.772152
61 DCZ 0.424242 0.880597
62 LDC 0.424242 0.880597
63 QUH 0.42 0.815789
64 FUH 0.42 0.815789
65 4TA 0.419048 0.743902
66 D3T 0.417722 0.847222
67 DT ME6 DT 0.415842 0.802632
68 5MD 0.411765 0.953125
69 ADS THS THS THS 0.411215 0.746988
70 DPB 0.407407 0.783784
71 TPE 0.406593 0.802632
72 B86 0.405797 0.84507
73 5BT 0.405797 0.84507
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2B8T; Ligand: THM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2b8t.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2B8T; Ligand: THM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2b8t.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2B8T; Ligand: THM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2b8t.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2B8T; Ligand: THM; Similar sites found: 176
This union binding pocket(no: 4) in the query (biounit: 2b8t.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1FZQ GDP 0.00127 0.45918 None
2 3AQ4 GDP 0.001816 0.44663 None
3 2CJW GDP 0.004138 0.43416 None
4 2X2T GAL NGA 0.02199 0.42802 None
5 1B0U ATP 0.003544 0.42432 None
6 1NN5 2DT 0.02471 0.411 None
7 3B7G ANP 0.002663 0.43872 0.896861
8 2CBZ ATP 0.0006482 0.49043 1.34529
9 2V57 PRL 0.01228 0.42312 1.57895
10 3CNL GNP 0.0008043 0.47457 1.79372
11 4YDS ATP 0.004139 0.44418 1.79372
12 2AWN ADP 0.00007522 0.54753 2.24215
13 3U6B GDP 0.002279 0.45197 2.24215
14 4IEE AGS 0.002854 0.44708 2.24215
15 4G5G GDP 0.00326 0.43922 2.24215
16 3U6K GDP 0.004543 0.43218 2.24215
17 2BVN GNP 0.01086 0.40218 2.24215
18 4MKG AP5 0.01661 0.40167 2.30415
19 4WEI GLC GAL 0.0111 0.42478 2.52708
20 3LRE ADP 0.0003361 0.50864 2.69058
21 3TK1 GDP 0.001512 0.46663 2.69058
22 2EFE GNH 0.002784 0.42908 2.69058
23 5GJC ATP 0.0002174 0.41487 2.69058
24 5FHD ADP ALF 0.003509 0.41331 2.69058
25 1OE0 TTP 0.004298 0.41285 2.69058
26 3R7F CP 0.02106 0.40946 2.69058
27 5VGR GDP 0.00817 0.40426 2.69058
28 4BQS ADP 0.006237 0.42546 2.84091
29 4BQS K2Q 0.004603 0.42226 2.84091
30 4B47 GDP 0.002211 0.45262 3.13901
31 2NCD ADP 0.004206 0.44653 3.13901
32 1U0J ADP 0.002989 0.44608 3.13901
33 5HCN GCP 0.001905 0.44565 3.13901
34 2ZFI ADP 0.007167 0.42251 3.13901
35 4R43 GDP 0.01129 0.41285 3.13901
36 3GXO MQA 0.02286 0.40172 3.13901
37 1A4R GNH 0.004314 0.4166 3.14136
38 1A4R GDP 0.005198 0.40943 3.14136
39 2WMO GTP 0.005804 0.41848 3.15789
40 1ZJ6 G3D 0.002388 0.44098 3.20856
41 4MKF AP5 0.013 0.40744 3.22581
42 4DID GDP 0.004248 0.42907 3.28947
43 1Z0F GDP 0.003841 0.43115 3.35196
44 1T5C ADP 0.0007204 0.48802 3.58744
45 1XP8 AGS 0.001591 0.45977 3.58744
46 1I4D GDP 0.005047 0.43469 3.58744
47 1SQ5 ADP 0.004755 0.42673 3.58744
48 4U60 SIA 0.02557 0.41466 3.58744
49 3BFV ADP 0.01195 0.41164 3.58744
50 4U60 SIA GAL NGA 0.03124 0.40893 3.58744
51 1UJ2 ADP 0.006155 0.40619 3.58744
52 1UJ2 C5P 0.006533 0.40508 3.58744
53 2X77 GDP 0.001587 0.44942 3.7037
54 3N5C GDP 0.002094 0.44859 3.7037
55 4TTQ ATP 0.002149 0.44804 3.72093
56 1TLG GAL 0.00786 0.42666 4
57 1G6H ADP 0.0003383 0.50841 4.03587
58 4WZ6 ATP 0.001813 0.46612 4.03587
59 3DKP ADP 0.001859 0.45111 4.03587
60 1SKQ GDP 0.002996 0.44602 4.03587
61 3BOS CDP 0.002966 0.44122 4.03587
62 4NON GDP 0.003107 0.44023 4.03587
63 1NHX PEP 0.0106 0.41334 4.03587
64 1NHX FTB 0.01111 0.41334 4.03587
65 4P32 ADP 0.003303 0.411 4.03587
66 5X40 ACP 0.005295 0.40418 4.03587
67 1VHT BA3 0.00661 0.41585 4.4843
68 2NGR GDP 0.007447 0.41745 4.70085
69 5BQ5 ADP BEF 0.004586 0.42324 4.7619
70 2WJG GDP 0.005237 0.42917 4.78723
71 2WHX ADP 0.00009358 0.5342 4.93274
72 1KK1 GNP 0.00391 0.44024 4.93274
73 2IYL GDP 0.006779 0.42369 4.93274
74 2JLR ANP 0.0005851 0.41829 4.93274
75 1JWY ADP 0.009942 0.41146 4.93274
76 3UIE ANP 0.001036 0.45327 5
77 5KSP GDP 0.009139 0.4132 5.26316
78 4AG5 ADP 0.0004476 0.49911 5.38117
79 2XT3 ADP 0.0009553 0.48347 5.38117
80 1JJV ATP 0.001342 0.47349 5.38117
81 3DC4 ADP 0.002435 0.45601 5.38117
82 2BIF SIN 0.002335 0.44309 5.38117
83 4LC1 GDP 0.003096 0.4403 5.38117
84 2WIC GNP 0.004575 0.42753 5.38117
85 2BIF ANP 0.00452 0.42018 5.38117
86 3RC3 ANP 0.009994 0.41981 5.38117
87 1G7S GDP 0.007628 0.41695 5.38117
88 2CXG GLC GLC 0.02253 0.4045 5.38117
89 1S9D GDP 0.003259 0.43455 5.41872
90 1UKZ ADP 0.008985 0.40708 5.41872
91 1Y63 ADP 0.004084 0.43444 5.43478
92 1F6B GDP 0.003141 0.43531 5.55556
93 3BY8 MLT 0.02526 0.40365 5.6338
94 1S8F GDP 0.009281 0.40898 5.64972
95 5L3V GDP 0.005807 0.41847 5.8296
96 4QM7 GTP 0.0004632 0.48051 5.84795
97 3W5J GDP 0.000838 0.48705 5.88235
98 1M7G ADP 0.001226 0.43927 6.16114
99 1M7G ADX 0.001749 0.43552 6.16114
100 2OG2 MLI 0.0001067 0.55226 6.27803
101 1GOJ ADP 0.000261 0.51544 6.27803
102 3B9Q MLI 0.0004611 0.515 6.27803
103 2D2F ADP 0.008806 0.43071 6.27803
104 2G77 AF3 0.02403 0.40755 6.27803
105 1G6O ADP 0.01295 0.40224 6.27803
106 2G77 GDP 0.01002 0.40031 6.27803
107 4TMK T5A 0.006484 0.41331 6.57277
108 4DCT GDP 0.002952 0.43659 6.72646
109 5MZN ADP 0.008207 0.42889 6.72646
110 3A1S GDP 0.006138 0.42145 6.72646
111 1D2E GDP 0.007683 0.40903 6.72646
112 4PC3 GDP 0.008019 0.40818 6.72646
113 2QZ4 ADP 0.01175 0.40419 6.72646
114 3H86 AP5 0.005467 0.41777 6.77083
115 2W58 ADP 0.0003617 0.50957 6.93069
116 3NHB ADP 0.0007605 0.48618 7.17489
117 5GOE GDP 0.008238 0.41139 7.17489
118 3PQC GDP 0.009265 0.40902 7.17949
119 3GJ0 GDP 0.004767 0.43116 7.23982
120 3GJ7 GDP 0.005299 0.42892 7.23982
121 3GJ4 GDP 0.00562 0.42767 7.23982
122 3GJ8 GDP 0.006503 0.42025 7.23982
123 3GJ5 GDP 0.007055 0.41857 7.23982
124 3CH5 GDP 0.008353 0.41507 7.40741
125 3B5J 12D 0.002246 0.45782 7.62332
126 5XDR ADP 0.006371 0.42068 7.68116
127 5H56 ADP 0.003725 0.4199 7.69231
128 5H56 TYD 0.003725 0.4199 7.69231
129 3IIJ ADP 0.00588 0.42671 7.77778
130 3QF7 ANP 0.0006975 0.42735 8
131 2PL3 ADP 0.0009886 0.4701 8.07175
132 2V7Q ATP 0.002093 0.43908 8.07175
133 3LXR GDP 0.01072 0.40606 8.10811
134 1JJ7 ADP 0.0003973 0.50383 8.52018
135 4J0Q GDP 0.002161 0.45312 8.52018
136 2QN6 GDP 0.001739 0.45784 8.60215
137 2JAQ DCP 0.00128 0.4212 8.78049
138 3A4M ADP 0.0002428 0.50738 8.84615
139 2A5J GDP 0.007061 0.41451 8.90052
140 3MD0 GDP 0.002925 0.44655 8.96861
141 3WY9 GDP 0.004999 0.43489 8.96861
142 3WYA GDP 0.004745 0.43126 8.96861
143 4HSE ADP 0.009194 0.41308 8.96861
144 1YRB GDP 0.009846 0.40412 8.96861
145 4ZNL BEF ADP 0.0007575 0.40207 8.96861
146 4QOS ADP 0.001425 0.44683 9.41704
147 2IS6 ADP 0.00588 0.42671 9.41704
148 3DZD ADP 0.01106 0.40182 9.41704
149 4CVN ADP 0.001606 0.4653 9.42408
150 2ZE7 AMP 0.001021 0.43777 9.86547
151 2ZE7 DST 0.001126 0.43766 9.86547
152 3VOZ 04A 0.04171 0.40276 9.86547
153 2OFW ADX 0.001152 0.45248 10.5769
154 4V0K GDP 0.002695 0.42184 11.2426
155 4A4Z ANP 0.001148 0.4613 12.1076
156 2PEZ GGZ 0.003404 0.42429 12.2905
157 2PEZ DAT 0.003404 0.42429 12.2905
158 1SVI GDP 0.003251 0.44425 12.5561
159 3FB4 AP5 0.009942 0.4117 12.5561
160 1V8K ANP 0.009173 0.41727 13.0045
161 5G41 AP5 0.01039 0.41556 13.0045
162 3KTA AP5 0.006673 0.41182 13.2948
163 3EF0 ALF 0.006578 0.44091 13.4529
164 3LN9 FLC 0.02796 0.41714 13.4529
165 4PPF FLC 0.000007867 0.59335 13.9013
166 1OXV ANP 0.00005996 0.4256 13.9013
167 1GXU 2HP 0.01345 0.40363 14.2857
168 2ZR9 DTP 0.0007452 0.47045 14.3498
169 2GGH NLQ 0.01203 0.40014 14.3498
170 3TBK ANP 0.0009768 0.47637 14.7982
171 1JI0 ATP 0.0002764 0.5045 15.2466
172 1YQT ADP 0.001571 0.46951 15.2466
173 2GDJ ANP 0.002219 0.44736 15.6951
174 2PFZ PCA 0.03158 0.40043 16.5919
175 4DKX GDP 0.002974 0.44116 17.1296
176 2DPY ADP 0.005116 0.43945 17.4888
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