Receptor
PDB id Resolution Class Description Source Keywords
1CY7 2.4 Å EC: 5.99.1.2 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONO ESCHERICHIA COLI DNA TOPOISOMERASE RELAXING ENZYME ISOMERASE
Ref.: PROTEIN-NUCLEOTIDE INTERACTIONS IN E. COLI DNA TOPO I. NAT.STRUCT.BIOL. V. 6 961 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:700;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
TMP A:600;
A:601;
A:602;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
322.208 C10 H15 N2 O8 P CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1CY2 2.3 Å EC: 5.99.1.2 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH TPTPTP3' ESCHERICHIA COLI DNA TOPOISOMERASE RELAXING ENZYME ISOMERASE
Ref.: PROTEIN-NUCLEOTIDE INTERACTIONS IN E. COLI DNA TOPO I. NAT.STRUCT.BIOL. V. 6 961 1999
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1CY0 - A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
2 1CY6 - T3P C10 H15 N2 O8 P CC1=CN(C(=....
3 1CY1 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
4 1CY8 - T3P C10 H15 N2 O8 P CC1=CN(C(=....
5 1CY7 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
6 1CY2 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1CY0 - A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
2 1CY6 - T3P C10 H15 N2 O8 P CC1=CN(C(=....
3 1CY1 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
4 1CY8 - T3P C10 H15 N2 O8 P CC1=CN(C(=....
5 1CY7 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
6 1CY2 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1CY0 - A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
2 1CY6 - T3P C10 H15 N2 O8 P CC1=CN(C(=....
3 1CY1 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
4 1CY8 - T3P C10 H15 N2 O8 P CC1=CN(C(=....
5 1CY7 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
6 1CY2 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TMP; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 TMP 1 1
2 TYD 0.80597 0.985714
3 TTP 0.760563 0.985714
4 UFP 0.716418 0.917808
5 TBD 0.708333 0.945205
6 5HU 0.705882 0.957747
7 BRU 0.705882 0.917808
8 5IU 0.695652 0.917808
9 THM 0.693548 0.859155
10 LLT 0.693548 0.859155
11 NYM 0.671429 0.971831
12 FDM 0.671429 0.931507
13 THP 0.661972 0.985507
14 TLO 0.654321 0.931507
15 0DN 0.646154 0.84507
16 ATM 0.64 0.906667
17 BVP 0.64 0.957747
18 DAU 0.635294 0.918919
19 18T 0.623529 0.918919
20 1JB 0.623529 0.918919
21 TRH 0.623529 0.918919
22 3R2 0.623529 0.906667
23 TDX 0.623529 0.931507
24 DWN 0.609195 0.894737
25 T3Q 0.609195 0.894737
26 3YN 0.609195 0.918919
27 T3F 0.609195 0.894737
28 T46 0.602273 0.918919
29 0N2 0.602273 0.883117
30 T3P 0.6 0.957143
31 DT DT DT DT DT 0.597701 0.958333
32 MMF 0.595506 0.894737
33 0FX 0.595506 0.894737
34 AKM 0.593407 0.873418
35 UMP 0.583333 0.956522
36 DU 0.583333 0.956522
37 QDM 0.582418 0.883117
38 DT DT PST 0.577778 0.893333
39 FNF 0.576087 0.906667
40 JHZ 0.576087 0.871795
41 1YF 0.576087 0.906667
42 TXS 0.575342 0.8
43 4TG 0.569892 0.906667
44 T3S 0.56 0.8
45 2DT 0.555556 0.971429
46 ATY 0.548781 0.931507
47 DDN 0.547945 0.956522
48 AZD 0.535714 0.894737
49 FUH 0.53 0.894737
50 QUH 0.53 0.894737
51 T5A 0.524272 0.829268
52 DT DT DT 0.52381 0.890411
53 DT ME6 DT 0.509804 0.881579
54 DCM 0.506494 0.890411
55 DC 0.506494 0.890411
56 AZZ 0.5 0.789474
57 4TA 0.495327 0.817073
58 ABT 0.483516 0.871795
59 QBT 0.480519 0.915493
60 WMJ 0.477778 0.75
61 7SG 0.474138 0.851852
62 TQP 0.474138 0.851852
63 T4K 0.470085 0.841463
64 T5K 0.470085 0.841463
65 DUD 0.469136 0.942857
66 UMC 0.467532 0.901408
67 D3T 0.464286 0.957747
68 TPE 0.463158 0.881579
69 D4M 0.461538 0.927536
70 ID2 0.452055 0.786667
71 UC5 0.451219 0.929577
72 DUT 0.447059 0.942857
73 DUP 0.44186 0.916667
74 DUN 0.440476 0.916667
75 ADS THS THS THS 0.433628 0.776471
76 DT MA7 DT 0.42623 0.807229
77 8OG 0.425287 0.82716
78 BVD 0.423077 0.821918
79 74X 0.42 0.72093
80 74W 0.42 0.72093
81 5FU 0.4125 0.84
82 D4D 0.411765 0.914286
83 PAX 0.408333 0.839506
84 YYY 0.406977 0.878378
85 DA DT DA DA 0.404959 0.82716
86 BTD 0.404762 0.759494
87 DPB 0.404494 0.890411
88 DUT MG 0.404494 0.876712
89 5BU 0.402439 0.84
90 3DT 0.4 0.821918
91 DUS 0.4 0.820513
92 UMP AF3 PO4 0.4 0.842105
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1CY2; Ligand: TMP; 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: 1cy2.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1CY2; Ligand: TMP; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 1cy2.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5AMC GLY NIY 0.005268 0.41895 3.50584
2 2ZB3 NDP 0.01329 0.41962 3.96601
3 5BU2 RIB 0.003251 0.42647 5.06608
4 1DCP HBI 0.01334 0.4062 11.5385
5 1GS5 NLG 0.02949 0.40661 14.7287
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