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Receptor
PDB id Resolution Class Description Source Keywords
4D7M 1.55 Å NON-ENZYME: TRANSCRIPT_TRANSLATE TETR(D) IN COMPLEX WITH ANHYDROTETRACYCLINE AND MAGNESIUM ESCHERICHIA COLI TRANSCRIPTION ANTIBIOTIC RESISTANCE TETR
Ref.: TETRACYCLINE REPRESSOR ALLOSTERY DOES NOT DEPEND ON DIVALENT METAL RECOGNITION. BIOCHEMISTRY V. 53 7990 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:223;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
TDC A:222;
Valid;
none;
Ka = 980000000000 M^-1
426.419 C22 H22 N2 O7 Cc1c2...
SO4 A:301;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
CL A:305;
A:304;
A:302;
A:303;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4D7M 1.55 Å NON-ENZYME: TRANSCRIPT_TRANSLATE TETR(D) IN COMPLEX WITH ANHYDROTETRACYCLINE AND MAGNESIUM ESCHERICHIA COLI TRANSCRIPTION ANTIBIOTIC RESISTANCE TETR
Ref.: TETRACYCLINE REPRESSOR ALLOSTERY DOES NOT DEPEND ON DIVALENT METAL RECOGNITION. BIOCHEMISTRY V. 53 7990 2014
Members (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 291 families.
1 1ORK Kd = 1.56 nM ATC C25 H30 N4 O8 CN(C)CC(=O....
2 5FKK - TDC C22 H22 N2 O7 Cc1c2cccc(....
3 2TCT Ka ~ 10000000 M^-1 CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
4 5FKN - TDC C22 H22 N2 O7 Cc1c2cccc(....
5 2VKV Ka = 45000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
6 2X9D - ITC C22 H23 Cl N2 O8 C[C@@]1(c2....
7 4D7M Ka = 980000000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
8 5FKO - TDC C22 H22 N2 O7 Cc1c2cccc(....
9 2FJ1 - CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
10 5FKL - TDC C22 H22 N2 O7 Cc1c2cccc(....
11 2XB5 - I7T C21 H21 I N2 O7 CN(C)[C@H]....
12 2TRT - TAC C22 H24 N2 O8 C[C@]1(c2c....
13 4D7N Ka = 23000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
14 5FKM - TDC C22 H22 N2 O7 Cc1c2cccc(....
15 2VKE - TAC C22 H24 N2 O8 C[C@]1(c2c....
16 2O7O - DXT C22 H24 N2 O8 C[C@H]1c2c....
17 3FK7 Kd = 0.75 nM 4DM C20 H17 N O7 Cc1c2cccc(....
18 2X6O - 2TC C22 H21 Cl N2 O7 C[C@@]1(c2....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 2VPR - TDC C22 H22 N2 O7 Cc1c2cccc(....
2 1ORK Kd = 1.56 nM ATC C25 H30 N4 O8 CN(C)CC(=O....
3 5FKK - TDC C22 H22 N2 O7 Cc1c2cccc(....
4 2TCT Ka ~ 10000000 M^-1 CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
5 5FKN - TDC C22 H22 N2 O7 Cc1c2cccc(....
6 2VKV Ka = 45000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
7 2X9D - ITC C22 H23 Cl N2 O8 C[C@@]1(c2....
8 4D7M Ka = 980000000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
9 5FKO - TDC C22 H22 N2 O7 Cc1c2cccc(....
10 2FJ1 - CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
11 5FKL - TDC C22 H22 N2 O7 Cc1c2cccc(....
12 2XB5 - I7T C21 H21 I N2 O7 CN(C)[C@H]....
13 2TRT - TAC C22 H24 N2 O8 C[C@]1(c2c....
14 4D7N Ka = 23000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
15 5FKM - TDC C22 H22 N2 O7 Cc1c2cccc(....
16 2VKE - TAC C22 H24 N2 O8 C[C@]1(c2c....
17 2O7O - DXT C22 H24 N2 O8 C[C@H]1c2c....
18 3FK7 Kd = 0.75 nM 4DM C20 H17 N O7 Cc1c2cccc(....
19 2X6O - 2TC C22 H21 Cl N2 O7 C[C@@]1(c2....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 2VPR - TDC C22 H22 N2 O7 Cc1c2cccc(....
2 1ORK Kd = 1.56 nM ATC C25 H30 N4 O8 CN(C)CC(=O....
3 5FKK - TDC C22 H22 N2 O7 Cc1c2cccc(....
4 2TCT Ka ~ 10000000 M^-1 CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
5 5FKN - TDC C22 H22 N2 O7 Cc1c2cccc(....
6 2VKV Ka = 45000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
7 2X9D - ITC C22 H23 Cl N2 O8 C[C@@]1(c2....
8 4D7M Ka = 980000000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
9 5FKO - TDC C22 H22 N2 O7 Cc1c2cccc(....
10 2FJ1 - CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
11 5FKL - TDC C22 H22 N2 O7 Cc1c2cccc(....
12 2XB5 - I7T C21 H21 I N2 O7 CN(C)[C@H]....
13 2TRT - TAC C22 H24 N2 O8 C[C@]1(c2c....
14 4D7N Ka = 23000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
15 5FKM - TDC C22 H22 N2 O7 Cc1c2cccc(....
16 2VKE - TAC C22 H24 N2 O8 C[C@]1(c2c....
17 2O7O - DXT C22 H24 N2 O8 C[C@H]1c2c....
18 3FK7 Kd = 0.75 nM 4DM C20 H17 N O7 Cc1c2cccc(....
19 2X6O - 2TC C22 H21 Cl N2 O7 C[C@@]1(c2....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TDC; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 TDC 1 1
2 4DM 0.581395 0.762712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D7M; Ligand: TDC; Similar sites found with APoc: 133
This union binding pocket(no: 1) in the query (biounit: 4d7m.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
1 5NNT DPV None
2 2VWA PTY None
3 2WOR 2AN None
4 6BJO DUY None
5 2YLD CMO None
6 2CB8 MYA None
7 5Y02 HBX None
8 1MID LAP None
9 5AZC PGT 1.84332
10 2VDY HCY 1.84332
11 2JHP GUN 2.30415
12 5G6U TRP 2.30415
13 4HBM 0Y7 2.5
14 3TDC 0EU 2.76498
15 3X01 AMP 2.76498
16 4COQ SAN 2.76498
17 2EAE FUL 2.76498
18 3WWC BUA 2.76498
19 5V4R MGT 3.08642
20 5C9J DAO 3.22581
21 4UCC ZKW 3.22581
22 5K8P 6R8 3.22581
23 2FDW D3G 3.22581
24 4V1F BQ1 3.48837
25 5XNA SHV 3.62319
26 5I8F ML1 3.63636
27 2BHW NEX 3.68664
28 6CB2 OLC 3.68664
29 4G86 BNT 3.68664
30 1TV5 N8E 3.68664
31 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.68664
32 6BR8 6OU 3.68664
33 4Y9T PA1 3.68664
34 5FQK 6NT 3.68664
35 5HCN DAO 3.68664
36 6BR8 PGV 3.68664
37 4REF 3N0 3.68664
38 2GN2 C5P 3.68664
39 2Q8G AZX 4.14747
40 4EKQ NPO 4.14747
41 5CHR 4NC 4.37956
42 6BR9 PGV 4.60829
43 5W3Y ACO 4.60829
44 5WSY 7UC 4.62428
45 1DTL BEP 4.96894
46 1GNI OLA 5.06912
47 1U25 IHS 5.06912
48 2E9L PLM 5.06912
49 5LX9 OLB 5.52995
50 2OZ5 7XY 5.52995
51 3SP6 IL2 5.52995
52 5W7B MYR 5.67376
53 3ZPG 5GP 5.99078
54 5CX6 CDP 5.99078
55 2D5X L35 6.16438
56 4DE3 DN8 6.45161
57 3NB0 G6P 6.45161
58 3NFD COA 6.53595
59 6BVK EAV 6.58683
60 6D5V FVY 6.58683
61 6BVM EBV 6.58683
62 6BVI EC4 6.58683
63 6BVL EBY 6.58683
64 6BVJ EAS 6.58683
65 6D5M FW4 6.58683
66 6D5L FW7 6.58683
67 6D5J FV4 6.58683
68 6D5H FV7 6.58683
69 6D59 FVJ 6.58683
70 2PRG BRL 6.81818
71 3HYW DCQ 6.91244
72 3TL1 JRO 6.91824
73 4O4Z N2O 7.14286
74 3O01 DXC 7.37327
75 5OSW DIU 7.37327
76 4Q0A 4OA 7.37327
77 4NKW PLO 7.37327
78 4JX1 CAH 7.37327
79 4QAG F95 7.5188
80 4RYV ZEA 7.74194
81 3W54 RNB 7.8341
82 3LXI CAM 7.8341
83 1HBK MYR 7.86517
84 4G7A AZM 8.29493
85 3ROE THM 8.29493
86 5OCA 9QZ 8.75576
87 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 8.75576
88 4XCP PLM 8.82353
89 3RV5 DXC 8.98876
90 3E70 GDP 9.21659
91 1YYE 196 9.21659
92 1U3R 338 9.21659
93 3OLL EST 9.21659
94 4V3I ASP LEU THR ARG PRO 9.33852
95 2GWH PCI 9.67742
96 1M2Z BOG 10.1382
97 6DIO CIT 10.1382
98 5N26 CPT 10.4396
99 4YSX E23 10.5991
100 4XCZ T3Q 11.0599
101 2BCG GER 11.165
102 3KO0 TFP 11.8812
103 5C1M OLC 12
104 4RJD TFP 12.1212
105 6GMN F4E 12.5
106 5OM2 DXT 12.9032
107 5TVI MYR 13.0435
108 5TVI O8N 13.0435
109 4G8R 96P 13.3641
110 5Z84 CHD 14.1176
111 5ZCO CHD 14.1176
112 5W97 CHD 14.1176
113 1NF8 BOG 14.4928
114 3FAL REA 14.7465
115 1T0S BML 15.1163
116 4TV1 36M 15.2074
117 4TUZ 36J 15.2074
118 5HYR EST 15.2074
119 4MG8 27J 15.2074
120 4MGA 27L 15.2074
121 5WGD EST 15.2074
122 3UUD EST 15.2074
123 5WGQ EST 15.2074
124 5DXE EST 15.2074
125 4MGB XDH 15.2074
126 4MG7 27H 15.2074
127 4F4S EFO 15.7895
128 4WGF HX2 16.0976
129 1JH7 UVC 16.9312
130 4OGQ 7PH 17.6471
131 4OGQ UMQ 17.6471
132 4OGQ 1O2 17.6471
133 3B6C SDN 41.0138
Pocket No.: 2; Query (leader) PDB : 4D7M; Ligand: TDC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4d7m.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
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