Receptor
PDB id Resolution Class Description Source Keywords
3IMJ 2.02 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN IN COMPLEX WITH A CYCLOPROPYL-CONSTRAINED AC-PTYR-ILE-ASN-NH2 TRIPEPTIDE MIMI HOMO SAPIENS LIGAND PREORGANIZATION PEPTIDE MIMICS GOLGI APPARATUS HOSINTERACTION PHOSPHOPROTEIN SH2 DOMAIN SH3 DOMAIN SIGNALPROTEIN-PSEUDOPEPTIDE LIGAND COMPLEX SIGNALING PROTEIN-PEPCOMPLEX
Ref.: THERMODYNAMIC AND STRUCTURAL EFFECTS OF CONFORMATIO CONSTRAINTS IN PROTEIN-LIGAND INTERACTIONS. ENTROPI PARADOXY ASSOCIATED WITH LIGAND PREORGANIZATION. J.AM.CHEM.SOC. V. 131 16758 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AYI A:1;
B:1;
Valid;
Valid;
none;
none;
Ka = 2100000 M^-1
541.491 C22 H32 N5 O9 P CC[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6WM1 1.8 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN IN COMPLEX WITH A T AC-PY-AC6C-N-PHENYLPROPYL HOMO SAPIENS GRB2 SH2 LIGAND PREORGANIZATION PEPTIDE BINDING PROTEIN
Ref.: SOME THERMODYNAMIC EFFECTS OF VARYING NONPOLAR SURF PROTEIN-LIGAND INTERACTIONS. EUR.J.MED.CHEM. V. 208 12771 2020
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 3IMJ Ka = 2100000 M^-1 AYI C22 H32 N5 O9 P CC[C@H](C)....
2 3C7I Ka = 440000 M^-1 TVN C21 H32 N5 O9 P CC(C)[C@@H....
3 3S8O Ka = 6960000 M^-1 ACE PTR 02K ASN NH2 n/a n/a
4 3IN8 Ka = 400000 M^-1 FYI C22 H34 N5 O9 P CC[C@H](C)....
5 1BMB ic50 = 0.7 uM LYS PRO PHE PTR VAL ASN VAL GLU PHE n/a n/a
6 3KFJ Ka = 300000 M^-1 YEN C21 H30 N5 O11 P CNC(=O)C[C....
7 6WM1 Ka = 26000000 M^-1 ACE PTR 02K ASN PRA n/a n/a
8 6WO2 Ka = 16000000 M^-1 ACE PTR 02K ASN U67 n/a n/a
9 1FYR ic50 = 2.4 uM ACE PTR VAL ASN VAL n/a n/a
10 3S8L Ka = 430000 M^-1 ACE PTR 192 ASN NH2 n/a n/a
11 3IN7 Ka = 1200000 M^-1 AYQ C21 H29 N6 O10 P CNC(=O)[C@....
12 4P9V Kd = 0.154 uM PHQ PTR 02K ASN NH2 n/a n/a
13 3OVE Ka = 3700000 M^-1 ACT PTR 03E ASN NH2 n/a n/a
14 1BM2 ic50 = 0.11 uM ACE SLZ PTR VAL ASN VAL PRO n/a n/a
15 4P9Z Kd = 87.7 nM NMI PTR 02K ASN NH2 n/a n/a
16 3OV1 Ka = 160000 M^-1 ACT PTR 1AC ASN NH2 n/a n/a
17 2HUW Ka = 1000000 M^-1 YVN C21 H30 N5 O9 P CC(C)[C@@H....
18 3N8M Ka = 6500000 M^-1 6NA PTR VAL ASN VAL 9PR n/a n/a
19 3S8N Ka = 1610000 M^-1 ACE PTR AC5 ASN NH2 n/a n/a
20 3IMD Ka = 560000 M^-1 FYQ C21 H31 N6 O10 P CNC(=O)C[C....
21 3N84 - PTR VAL ASN VAL PRO 011 n/a n/a
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 3IMJ Ka = 2100000 M^-1 AYI C22 H32 N5 O9 P CC[C@H](C)....
2 3C7I Ka = 440000 M^-1 TVN C21 H32 N5 O9 P CC(C)[C@@H....
3 3S8O Ka = 6960000 M^-1 ACE PTR 02K ASN NH2 n/a n/a
4 3IN8 Ka = 400000 M^-1 FYI C22 H34 N5 O9 P CC[C@H](C)....
5 1BMB ic50 = 0.7 uM LYS PRO PHE PTR VAL ASN VAL GLU PHE n/a n/a
6 3KFJ Ka = 300000 M^-1 YEN C21 H30 N5 O11 P CNC(=O)C[C....
7 6WM1 Ka = 26000000 M^-1 ACE PTR 02K ASN PRA n/a n/a
8 3IMD Ka = 560000 M^-1 FYQ C21 H31 N6 O10 P CNC(=O)C[C....
9 3N84 - PTR VAL ASN VAL PRO 011 n/a n/a
10 3MXY Kd = 384.8 nM GLN ASN GLY PTR VAL ASN PRO THR TYR n/a n/a
11 1JYQ Kd = 2 nM MAZ PTR PTM ASN n/a n/a
12 1ZFP ic50 = 26 nM BE2 GLU PTR ILE ASN GLN NH2 n/a n/a
13 2AOA - S1S C41 H46 N4 O10 c1ccc2c(c1....
14 1TZE ic50 = 0.148 uM LYS PRO PHE PTR VAL ASN VAL NH2 n/a n/a
50% Homology Family (67)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 3S9K - CIT C6 H8 O7 C(C(=O)O)C....
2 3IMJ Ka = 2100000 M^-1 AYI C22 H32 N5 O9 P CC[C@H](C)....
3 3IN8 Ka = 400000 M^-1 FYI C22 H34 N5 O9 P CC[C@H](C)....
4 1BMB ic50 = 0.7 uM LYS PRO PHE PTR VAL ASN VAL GLU PHE n/a n/a
5 3KFJ Ka = 300000 M^-1 YEN C21 H30 N5 O11 P CNC(=O)C[C....
6 6WM1 Ka = 26000000 M^-1 ACE PTR 02K ASN PRA n/a n/a
7 6WO2 Ka = 16000000 M^-1 ACE PTR 02K ASN U67 n/a n/a
8 1FYR ic50 = 2.4 uM ACE PTR VAL ASN VAL n/a n/a
9 3S8L Ka = 430000 M^-1 ACE PTR 192 ASN NH2 n/a n/a
10 3IN7 Ka = 1200000 M^-1 AYQ C21 H29 N6 O10 P CNC(=O)[C@....
11 4P9V Kd = 0.154 uM PHQ PTR 02K ASN NH2 n/a n/a
12 3OVE Ka = 3700000 M^-1 ACT PTR 03E ASN NH2 n/a n/a
13 1BM2 ic50 = 0.11 uM ACE SLZ PTR VAL ASN VAL PRO n/a n/a
14 4P9Z Kd = 87.7 nM NMI PTR 02K ASN NH2 n/a n/a
15 3OV1 Ka = 160000 M^-1 ACT PTR 1AC ASN NH2 n/a n/a
16 2HUW Ka = 1000000 M^-1 YVN C21 H30 N5 O9 P CC(C)[C@@H....
17 3N8M Ka = 6500000 M^-1 6NA PTR VAL ASN VAL 9PR n/a n/a
18 3S8N Ka = 1610000 M^-1 ACE PTR AC5 ASN NH2 n/a n/a
19 3IMD Ka = 560000 M^-1 FYQ C21 H31 N6 O10 P CNC(=O)C[C....
20 3N84 - PTR VAL ASN VAL PRO 011 n/a n/a
21 1A1B Kd = 0.4 uM ACE PTR GLU DIP n/a n/a
22 1NZV Kd = 0.4 uM PRO GLN PTR ILE PTR VAL PRO ALA n/a n/a
23 1O4L ic50 > 40 mM CIT C6 H8 O7 C(C(=O)O)C....
24 1SHA - PTR VAL PRO MET LEU n/a n/a
25 1F1W - SER PTR VAL ASN VAL GLN ASN n/a n/a
26 1O4P ic50 = 2.5 mM 791 C9 H8 O4 c1ccc(cc1)....
27 1O49 ic50 = 437 nM 493 C32 H36 N3 O9 P CC(=O)N[C@....
28 1O47 ic50 = 4 nM 822 C31 H34 F2 N3 O6 P CC(=O)N[C@....
29 1A1A - ACE PTH GLU DIP n/a n/a
30 1SHB - PTR LEU ARG VAL ALA n/a n/a
31 1O4B ic50 = 2000 nM 876 C30 H35 N3 O9 P2 CC(=O)N[C@....
32 1IS0 Kd = 0.1 uM AY0 GLU GLU ILE n/a n/a
33 1A1E Kd = 1 uM ACE PTR GLU DIY n/a n/a
34 4F5B - PTR C9 H12 N O6 P c1cc(ccc1C....
35 1O4J ic50 = 4.4 mM IS2 C9 H12 N O4 P CCc1ccc(cc....
36 1BKM - 1C5 C26 H39 N4 O10 P CC(=O)N[C@....
37 1O4Q ic50 = 3.2 mM 256 C8 H8 O5 S c1ccc(cc1)....
38 1SKJ ic50 = 7 uM UR2 C25 H38 N3 O10 P CN(CCCC1CC....
39 1A1C Kd = 0.4 uM ACE PTR GLU DIX n/a n/a
40 1O4H ic50 = 3.6 mM 772 C10 H7 N2 O4 P c1cc2ccc(n....
41 1P13 - CYS ASP PTR ALA ASN PHE LYS n/a n/a
42 1KC2 Kd = 0.21 uM PRO GLN PTR GLU GLU ILE PRO ILE n/a n/a
43 1O4R ic50 = 3.9 mM 787 C7 H10 O6 P2 c1ccc(cc1)....
44 1O46 ic50 = 10 nM 903 C35 H36 F N3 O9 CC(=O)N[C@....
45 1NZL Kd = 0.07 uM PRO GLN PTR GLU PTR ILE PRO ALA n/a n/a
46 1O4M ic50 > 40 mM MLA C3 H4 O4 C(C(=O)O)C....
47 1O4F ic50 = 0.3 mM 790 C9 H12 N O4 P c1cc2c(c(c....
48 1O42 ic50 = 9 nM 843 C30 H34 N3 O7 P CC(=O)N[C@....
49 3MXY Kd = 384.8 nM GLN ASN GLY PTR VAL ASN PRO THR TYR n/a n/a
50 3WA4 - SER ASP PTR MET ASN MET THR PRO n/a n/a
51 3MXC Kd = 286.1 nM GLN ASN GLY PTR GLU ASN PRO THR TYR n/a n/a
52 3N7Y Ka = 10000000 M^-1 PTR VAL ASN VAL 011 n/a n/a
53 2AOB - S1S C41 H46 N4 O10 c1ccc2c(c1....
54 1JYR Kd = 18 nM ALA PRO SER PTR VAL ASN VAL GLN ASN n/a n/a
55 1ZFP ic50 = 26 nM BE2 GLU PTR ILE ASN GLN NH2 n/a n/a
56 2AOA - S1S C41 H46 N4 O10 c1ccc2c(c1....
57 1TZE ic50 = 0.148 uM LYS PRO PHE PTR VAL ASN VAL NH2 n/a n/a
58 1CWD - PRO GLU GLY ASP PM3 GLU GLU VAL LEU n/a n/a
59 1LKL Kd = 1540 nM ACE PTR GLU GLU GLY n/a n/a
60 1FBZ - CC1 C30 H41 N3 O10 P2 CC(=O)N[C@....
61 1IJR - CC0 C29 H38 N3 O10 P C[C@@H](c1....
62 1CWE - ACE GLN PM3 GLU GLU ILE PRO n/a n/a
63 5GJI - SER ASP PTR MET ASN MET THR PRO n/a n/a
64 5GJH - SER ASP PTR MET ASN MET THR PRO n/a n/a
65 1R1S - ACE PRO ASP PTR GLU ASN LEU n/a n/a
66 1R1P - ACE ASP ASP PTR VAL ASN VAL n/a n/a
67 1R1Q - ACE ARG GLU PTR VAL ASN VAL n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: AYI; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 AYI 1 1
2 YVN 0.807692 0.932203
3 AYQ 0.674419 0.932203
4 FYI 0.588889 0.932203
5 TVN 0.494737 0.883333
6 AY0 GLU GLU ILE 0.435185 0.822581
7 FYQ 0.415842 0.866667
8 YEN 0.411765 0.852459
Similar Ligands (3D)
Ligand no: 1; Ligand: AYI; Similar ligands found: 5
No: Ligand Similarity coefficient
1 ACE PTR 192 ASN NH2 0.8856
2 ACE PTR AC5 ASN NH2 0.8847
3 ACE PTR 02K ASN NH2 0.8825
4 ACT PTR 03E ASN NH2 0.8648
5 ACT PTR 1AC ASN NH2 0.8640
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6WM1; Ligand: ACE PTR 02K ASN PRA; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 6wm1.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1LCK GLU GLY GLN PTR GLN PRO GLN PRO ALA 45.2991
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