Receptor
PDB id Resolution Class Description Source Keywords
3N8M 2 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN IN COMPLEX WITH AN LIGAND HAVING THE SEQUENCE PYVNVP HOMO SAPIENS GRB2 SH2 DOMAIN LIGAND PREORGANIZATION MACROCYCLES MACROCLIGANDS PROTEIN BINDING-PEPTIDE COMPLEX
Ref.: THERMODYNAMIC AND STRUCTURAL EFFECTS OF MACROCYCLIZ A CONSTRAINING METHOD IN PROTEIN-LIGAND INTERACTION ACS MED.CHEM.LETT. V. 1 448 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6NA PTR VAL ASN VAL 9PR B:1;
 Valid;
 none;
 Ka = 6500000 M^-1
779.829 n/a P(=O)...
GOL B:9;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(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 (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6WO2 Ka = 16000000 M^-1 ACE PTR 02K ASN U67 n/a n/a
2 1FYR ic50 = 2.4 uM ACE PTR VAL ASN VAL n/a n/a
3 3S8L Ka = 430000 M^-1 ACE PTR 192 ASN NH2 n/a n/a
4 3IN7 Ka = 1200000 M^-1 AYQ C21 H29 N6 O10 P CNC(=O)[C@....
5 4P9V Kd = 0.154 uM PHQ PTR 02K ASN NH2 n/a n/a
6 3OVE Ka = 3700000 M^-1 ACT PTR 03E ASN NH2 n/a n/a
7 1BM2 ic50 = 0.11 uM ACE SLZ PTR VAL ASN VAL PRO n/a n/a
8 4P9Z Kd = 87.7 nM NMI PTR 02K ASN NH2 n/a n/a
9 3OV1 Ka = 160000 M^-1 ACT PTR 1AC ASN NH2 n/a n/a
10 2HUW Ka = 1000000 M^-1 YVN C21 H30 N5 O9 P CC(C)[C@@H....
11 3N8M Ka = 6500000 M^-1 6NA PTR VAL ASN VAL 9PR n/a n/a
12 3S8N Ka = 1610000 M^-1 ACE PTR AC5 ASN NH2 n/a n/a
13 3WA4 - SER ASP PTR MET ASN MET THR PRO n/a n/a
14 3MXC Kd = 286.1 nM GLN ASN GLY PTR GLU ASN PRO THR TYR n/a n/a
15 3N7Y Ka = 10000000 M^-1 PTR VAL ASN VAL 011 n/a n/a
16 2AOB - S1S C41 H46 N4 O10 c1ccc2c(c1....
17 1JYR Kd = 18 nM ALA PRO SER PTR VAL ASN VAL GLN ASN n/a n/a
18 5GJH - SER ASP PTR MET ASN MET THR PRO n/a n/a
19 1R1S - ACE PRO ASP PTR GLU ASN LEU n/a n/a
20 1R1P - ACE ASP ASP PTR VAL ASN VAL n/a n/a
21 1R1Q - ACE ARG GLU PTR VAL ASN VAL 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: 6NA PTR VAL ASN VAL 9PR; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 6NA PTR VAL ASN VAL 9PR 1 1
2 ALA PRO SER PTR VAL ASN VAL GLN ASN 0.572464 0.87013
3 LYS PRO PHE PTR VAL ASN VAL NH2 0.571429 0.893333
4 GLN ASN GLY PTR VAL ASN PRO THR TYR 0.557971 0.846154
5 LYS PRO PHE PTR VAL ASN VAL GLU PHE 0.532895 0.881579
6 PRO GLN PTR ILE PTR VAL PRO ALA 0.506944 0.868421
7 GLU VAL PTR GLU SER PRO 0.463768 0.831169
8 PTR VAL PRO MET LEU 0.463768 0.866667
9 GLN ASN GLY PTR GLU ASN PRO THR TYR 0.462585 0.842105
10 SER PTR VAL ASN VAL GLN ASN 0.462121 0.688312
11 SER ASP PTR MET ASN MET THR PRO 0.456376 0.860759
12 ARG VAL ILE PTR PHE VAL PRO LEU ASN ARG 0.455882 0.864865
13 PRO GLN PTR GLU PTR ILE PRO ALA 0.440789 0.855263
14 PRO GLN PTR GLU GLU ILE PRO ILE 0.434211 0.878378
15 ASP TYR ILE ASN THR ASN VAL LEU PRO 0.432432 0.813333
16 ACE LEU TYR ALA SER SER ASN PRO ALA PTR 0.423077 0.860759
17 ASP GLY PTR MET PRO 0.421429 0.855263
18 ACE GLU VAL ASN ALA PRO VAL LPD 0.407407 0.767123
19 GLU GLY GLN PTR GLN PRO GLN PRO ALA 0.403846 0.837838
Similar Ligands (3D)
Ligand no: 1; Ligand: 6NA PTR VAL ASN VAL 9PR; Similar ligands found: 0
No: Ligand Similarity coefficient
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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