Receptor
PDB id Resolution Class Description Source Keywords
1NC4 2.25 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF MONOCLONAL ANTIBODY 2D12.5 FAB COMPLEXE DOTA MUS MUSCULUS ANTIBODY-DOTA COMPLEX RARE EARTH DOTA METAL CHELATE GADOGAMMA TURN N-LINKED GLYCOSYLATION IMMUNE SYSTEM
Ref.: CRYSTAL STRUCTURES OF TWO COMPLEXES OF THE RARE-EARTH-DOTA-BINDING ANTIBODY 2D12.5: LIGAND GEN FROM A CHIRAL SYSTEM. J.AM.CHEM.SOC. V. 125 15039 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:504;
C:505;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
DOF B:500;
D:501;
Valid;
Valid;
none;
none;
submit data
539.536 C23 H33 N5 O10 c1cc(...
GD3 B:502;
D:503;
Invalid;
Invalid;
none;
none;
submit data
157.25 Gd [Gd+3...
NAG D:400;
Invalid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1NC4 2.25 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF MONOCLONAL ANTIBODY 2D12.5 FAB COMPLEXE DOTA MUS MUSCULUS ANTIBODY-DOTA COMPLEX RARE EARTH DOTA METAL CHELATE GADOGAMMA TURN N-LINKED GLYCOSYLATION IMMUNE SYSTEM
Ref.: CRYSTAL STRUCTURES OF TWO COMPLEXES OF THE RARE-EARTH-DOTA-BINDING ANTIBODY 2D12.5: LIGAND GEN FROM A CHIRAL SYSTEM. J.AM.CHEM.SOC. V. 125 15039 2003
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
2 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
3 5MES ic50 = 0.045 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
3 5DS8 - GLY 5CT GLY ALA n/a n/a
4 5DRN - 5CT C10 H23 N3 O3 C(CCNC[C@H....
5 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
6 1QKZ - ALA ASN GLY GLY ALA SER GLY GLN VAL LYS n/a n/a
7 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
8 2HVK - TBA C16 H36 N CCCC[N+](C....
9 5DUB - GLY 5GG GLY ALA n/a n/a
10 5MES ic50 = 0.045 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
11 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
12 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
13 5T85 - 44G C18 H35 O10 P CCCCCC(=O)....
14 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
15 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
16 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
17 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
18 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
19 2DWE - TBA C16 H36 N CCCC[N+](C....
20 3PGF - GLC GLC n/a n/a
21 1MJJ Kd = 1.83 nM HAL C23 H29 N2 O7 P c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DOF; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 DOF 1 1
2 DOE 0.578313 0.725806
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NC4; Ligand: DOF; Similar sites found: 59
This union binding pocket(no: 1) in the query (biounit: 1nc4.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1N5D NDP 0.03826 0.4074 1.86047
2 5XDT MB3 0.02935 0.41455 1.94805
3 5XDT GDP 0.03086 0.40711 1.94805
4 4QJR PIZ 0.01425 0.41925 2.04082
5 1ZDT PEF 0.01368 0.41766 2.07469
6 4D42 W0I 0.04339 0.42187 2.26244
7 4D42 NAP 0.04339 0.42187 2.26244
8 5T2Z 017 0.03772 0.40426 3.0303
9 4XFR CIT 0.00172 0.4306 3.16742
10 4XG0 CIT 0.00335 0.42894 3.25581
11 5E1M SAH 0.04774 0.40134 3.61991
12 5E1M PRO PRO LYS ARG ILE ALA 0.04774 0.40134 3.61991
13 3EEB IHP 0.02157 0.40084 3.82775
14 2VJ8 HA2 0.01892 0.43409 4.0724
15 4ZFL 4NK 0.032 0.40346 4.18605
16 2Y88 2ER 0.02666 0.41939 4.52489
17 1QX4 FAD 0.02941 0.41698 4.65116
18 3ZY6 GFB 0.02016 0.41168 5.11628
19 4AUT FAD 0.01861 0.42851 5.42986
20 1Y52 BTN 0.03376 0.41909 5.55556
21 1NYT NAP 0.02593 0.40849 5.5814
22 1MS9 LAT 0.02184 0.40125 5.5814
23 2E0N SAH 0.01144 0.41113 5.88235
24 4Q5M ROC 0.04422 0.40369 5.91133
25 2GBP BGC 0.01375 0.40773 6.04651
26 4B7X NAP 0.04826 0.40144 6.54762
27 4YOI 4F4 0.00534 0.43556 6.78733
28 4Q9N NAI 0.02778 0.41457 6.78733
29 1KKR 2AS 0.00702 0.40877 6.97674
30 2J7T 274 0.04373 0.40335 7.23982
31 1RO7 CSF 0.0358 0.40211 7.23982
32 3MN9 ATP 0.0301 0.40098 7.44186
33 5B48 TDN 0.03058 0.41055 7.69231
34 3U4L ATP 0.02662 0.40525 7.85714
35 2DM6 IMN 0.04651 0.40711 7.90698
36 2HK9 NAP 0.03757 0.40383 7.90698
37 1U7T NAD 0.0401 0.40197 7.90698
38 3EPO MP5 0.0244 0.40191 8.1448
39 1O2D NAP 0.04543 0.4006 8.37209
40 2VHW NAI 0.0379 0.40738 8.59729
41 1XTT U5P 0.00904 0.42022 8.83721
42 1JP4 AMP 0.02094 0.4054 8.83721
43 3FGC FMN 0.01252 0.42154 9.76744
44 5DV2 C5P 0.02484 0.40602 9.95475
45 2WSB NAD 0.03208 0.41657 10.2326
46 3KFL ME8 0.02411 0.41367 10.6977
47 2UZ2 BTN 0.005657 0.43118 11.3122
48 4EYG VNL 0.01743 0.40217 11.6279
49 2VHJ ADP 0.02485 0.40533 12.093
50 1EZ0 NAP 0.01722 0.42448 12.2172
51 2D1K ATP 0.02327 0.40725 12.5581
52 3U9Z ADP 0.02052 0.40608 12.5581
53 1RHC F42 ACN 0.04285 0.40111 14.4186
54 1IY8 NAD 0.02847 0.41186 14.8837
55 1U00 GLU LEU PRO PRO VAL LYS ILE HIS CYS 0.02384 0.40269 15.4185
56 1V97 MTE 0.0488 0.40988 16.7421
57 3FHQ BMA NGT MAN MAN 0.01644 0.40594 16.7421
58 2Q8Z NUP 0.01237 0.41903 19.9095
59 2BVD ISX 0.02147 0.40858 19.9095
Pocket No.: 2; Query (leader) PDB : 1NC4; Ligand: DOF; Similar sites found: 23
This union binding pocket(no: 2) in the query (biounit: 1nc4.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2QZZ EMF 0.04802 0.40974 1.86047
2 1XTP SAI 0.02367 0.40269 3.16742
3 3FSM 2NC 0.02746 0.41842 3.44828
4 4XJ7 ADN 0.01159 0.4072 3.61991
5 4POW OP1 0.0319 0.40102 3.61991
6 5E9G GLV 0.00535 0.40697 3.72093
7 1JIL 485 0.02901 0.40196 3.72093
8 3WQT ANP 0.02941 0.40156 3.72093
9 2PI8 NAG NAG NAG NAG NAG NAG 0.03622 0.40656 4.0724
10 2DC1 NAD 0.03405 0.40623 4.52489
11 4LWU 20U 0.01699 0.4059 7.05882
12 1WBI BTN 0.004363 0.43573 8.52713
13 1O7Q UDP 0.04581 0.40177 8.59729
14 1QV1 CZH 0.02143 0.41685 8.71795
15 1PJS SAH 0.02033 0.40426 8.83721
16 4B1M FRU FRU 0.009962 0.40171 9.72973
17 1CEL BGC IBZ 0.009792 0.40772 9.95475
18 2Q3O FMN 0.03455 0.4029 10.6977
19 3CX8 GSP 0.04249 0.40261 11.33
20 1U1B PAX 0.04989 0.40027 14.5161
21 4B1W ATP 0.0243 0.40685 15.625
22 3SSO SAH 0.03862 0.41146 15.8371
23 1L6O SER LEU LYS LEU MET THR THR VAL 0.0242 0.41259 20
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