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Receptor
PDB id Resolution Class Description Source Keywords
3IN7 2 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN IN COMPLEX WITH A CYCLOPROPYL-CONSTRAINED AC-PY-Q-N-NH2 TRIPEPTIDE MIMIC 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
AYQ A:1;
C:1;
Valid;
Valid;
none;
none;
Ka = 1200000 M^-1
556.463 C21 H29 N6 O10 P CNC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4P9Z 1.8 Å NON-ENZYME: SIGNAL_HORMONE GRB2 SH2 COMPLEXED WITH A PTYR-AC6C-ASN TRIPEPTIDE HOMO SAPIENS GRB2 SH2 CATION-PI INTERACTION SIGNALING PROTEIN-ANTAGONIS
Ref.: PROTEIN-LIGAND INTERACTIONS: PROBING THE ENERGETICS PUTATIVE CATION-PI INTERACTION. BIOORG.MED.CHEM.LETT. V. 24 3164 2014
Members (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 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 1FYR ic50 = 2.4 uM ACE PTR VAL ASN VAL n/a n/a
8 3S8L Ka = 430000 M^-1 ACE PTR 192 ASN NH2 n/a n/a
9 3IN7 Ka = 1200000 M^-1 AYQ C21 H29 N6 O10 P CNC(=O)[C@....
10 4P9V Kd = 0.154 uM PHQ PTR 02K ASN NH2 n/a n/a
11 3OVE Ka = 3700000 M^-1 ACT PTR 03E ASN NH2 n/a n/a
12 1BM2 ic50 = 0.11 uM ACE SLZ PTR VAL ASN VAL PRO n/a n/a
13 4P9Z Kd = 87.7 nM NMI PTR 02K ASN NH2 n/a n/a
14 3OV1 Ka = 160000 M^-1 ACT PTR 1AC ASN NH2 n/a n/a
15 2HUW Ka = 1000000 M^-1 YVN C21 H30 N5 O9 P CC(C)[C@@H....
16 3N8M Ka = 6500000 M^-1 6NA PTR VAL ASN VAL 9PR n/a n/a
17 3S8N Ka = 1610000 M^-1 ACE PTR AC5 ASN NH2 n/a n/a
18 3IMD Ka = 560000 M^-1 FYQ C21 H31 N6 O10 P CNC(=O)C[C....
19 3N84 - PTR VAL ASN VAL PRO 011 n/a n/a
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 1FYR ic50 = 2.4 uM ACE PTR VAL ASN VAL n/a n/a
2 3S8L Ka = 430000 M^-1 ACE PTR 192 ASN NH2 n/a n/a
3 3IN7 Ka = 1200000 M^-1 AYQ C21 H29 N6 O10 P CNC(=O)[C@....
4 4P9V Kd = 0.154 uM PHQ PTR 02K ASN NH2 n/a n/a
5 3OVE Ka = 3700000 M^-1 ACT PTR 03E ASN NH2 n/a n/a
6 1BM2 ic50 = 0.11 uM ACE SLZ PTR VAL ASN VAL PRO n/a n/a
7 4P9Z Kd = 87.7 nM NMI PTR 02K ASN NH2 n/a n/a
8 3OV1 Ka = 160000 M^-1 ACT PTR 1AC ASN NH2 n/a n/a
9 2HUW Ka = 1000000 M^-1 YVN C21 H30 N5 O9 P CC(C)[C@@H....
10 3N8M Ka = 6500000 M^-1 6NA PTR VAL ASN VAL 9PR n/a n/a
11 3S8N Ka = 1610000 M^-1 ACE PTR AC5 ASN NH2 n/a n/a
12 3IMD Ka = 560000 M^-1 FYQ C21 H31 N6 O10 P CNC(=O)C[C....
13 3N84 - PTR VAL ASN VAL PRO 011 n/a n/a
14 3WA4 - SER ASP PTR MET ASN MET THR n/a n/a
15 3MXC Kd = 286 nM GLN ASN GLY PTR GLU ASN PRO THR TYR n/a n/a
16 3N7Y Ka = 10000000 M^-1 PTR VAL ASN VAL 011 n/a n/a
17 2AOB - S1S C41 H46 N4 O10 c1ccc2c(c1....
18 1JYR Kd = 18 nM ALA PRO SER PTR VAL ASN VAL GLN ASN n/a n/a
19 1ZFP ic50 = 26 nM BE2 GLU PTR ILE ASN GLN NH2 n/a n/a
20 2AOA - S1S C41 H46 N4 O10 c1ccc2c(c1....
21 1TZE ic50 = 148 nM LYS PRO PHE PTR VAL ASN VAL NH2 n/a n/a
22 5GJH - SER ASP PTR MET ASN MET THR PRO n/a n/a
23 1R1S - ACE PRO ASP PTR GLU ASN LEU n/a n/a
24 1R1P - ACE ASP ASP PTR VAL ASN VAL n/a n/a
25 1R1Q - ACE ARG GLU PTR VAL ASN VAL n/a n/a
50% Homology Family (64)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 174 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 1FYR ic50 = 2.4 uM ACE PTR VAL ASN VAL n/a n/a
7 3S8L Ka = 430000 M^-1 ACE PTR 192 ASN NH2 n/a n/a
8 3IN7 Ka = 1200000 M^-1 AYQ C21 H29 N6 O10 P CNC(=O)[C@....
9 4P9V Kd = 0.154 uM PHQ PTR 02K ASN NH2 n/a n/a
10 3OVE Ka = 3700000 M^-1 ACT PTR 03E ASN NH2 n/a n/a
11 1BM2 ic50 = 0.11 uM ACE SLZ PTR VAL ASN VAL PRO n/a n/a
12 4P9Z Kd = 87.7 nM NMI PTR 02K ASN NH2 n/a n/a
13 3OV1 Ka = 160000 M^-1 ACT PTR 1AC ASN NH2 n/a n/a
14 2HUW Ka = 1000000 M^-1 YVN C21 H30 N5 O9 P CC(C)[C@@H....
15 3N8M Ka = 6500000 M^-1 6NA PTR VAL ASN VAL 9PR n/a n/a
16 3S8N Ka = 1610000 M^-1 ACE PTR AC5 ASN NH2 n/a n/a
17 3IMD Ka = 560000 M^-1 FYQ C21 H31 N6 O10 P CNC(=O)C[C....
18 3N84 - PTR VAL ASN VAL PRO 011 n/a n/a
19 1A1B Kd = 0.4 uM ACE PTR GLU DIP n/a n/a
20 1NZV Kd = 0.4 uM PRO GLN PTR ILE PTR VAL PRO ALA n/a n/a
21 1O4L ic50 > 40 mM CIT C6 H8 O7 C(C(=O)O)C....
22 1SHA - PTR VAL PRO MET LEU n/a n/a
23 1F1W - SER PTR VAL ASN VAL GLN ASN n/a n/a
24 1O4P ic50 = 2.5 mM 791 C9 H8 O4 c1ccc(cc1)....
25 1O49 ic50 = 437 nM 493 C32 H36 N3 O9 P CC(=O)N[C@....
26 1O47 ic50 = 4 nM 822 C31 H34 F2 N3 O6 P CC(=O)N[C@....
27 1A1A - ACE PTH GLU DIP n/a n/a
28 1SHB - PTR LEU ARG VAL ALA n/a n/a
29 1O4B ic50 = 2000 nM 876 C30 H35 N3 O9 P2 CC(=O)N[C@....
30 1IS0 Kd = 0.1 uM AY0 GLU GLU ILE n/a n/a
31 1A1E Kd = 1 uM ACE PTR GLU DIY n/a n/a
32 4F5B - PTR C9 H12 N O6 P c1cc(ccc1C....
33 1O4J ic50 = 4.4 mM IS2 C9 H12 N O4 P CCc1ccc(cc....
34 1BKM - 1C5 C26 H39 N4 O10 P CC(=O)N[C@....
35 1O4Q ic50 = 3.2 mM 256 C8 H8 O5 S c1ccc(cc1)....
36 1SKJ ic50 = 7 uM UR2 C25 H38 N3 O10 P CN(CCCC1CC....
37 1A1C Kd = 0.4 uM ACE PTR GLU DIX n/a n/a
38 1O4H ic50 = 3.6 mM 772 C10 H7 N2 O4 P c1cc2ccc(n....
39 1P13 - CYS ASP PTR ALA ASN PHE LYS n/a n/a
40 1KC2 Kd = 0.21 uM PRO GLN PTR GLU GLU ILE PRO ILE n/a n/a
41 1O4R ic50 = 3.9 mM 787 C7 H10 O6 P2 c1ccc(cc1)....
42 1O46 ic50 = 10 nM 903 C35 H36 F N3 O9 CC(=O)N[C@....
43 1NZL Kd = 0.07 uM PRO GLN PTR GLU PTR ILE PRO ALA n/a n/a
44 1O4M ic50 > 40 mM MLA C3 H4 O4 C(C(=O)O)C....
45 1O4F ic50 = 0.3 mM 790 C9 H12 N O4 P c1cc2c(c(c....
46 1O42 ic50 = 9 nM 843 C30 H34 N3 O7 P CC(=O)N[C@....
47 3MXY Kd = 384 nM GLN ASN GLY PTR VAL ASN PRO THR TYR n/a n/a
48 3WA4 - SER ASP PTR MET ASN MET THR n/a n/a
49 3MXC Kd = 286 nM GLN ASN GLY PTR GLU ASN PRO THR TYR n/a n/a
50 3N7Y Ka = 10000000 M^-1 PTR VAL ASN VAL 011 n/a n/a
51 2AOB - S1S C41 H46 N4 O10 c1ccc2c(c1....
52 1JYR Kd = 18 nM ALA PRO SER PTR VAL ASN VAL GLN ASN n/a n/a
53 1ZFP ic50 = 26 nM BE2 GLU PTR ILE ASN GLN NH2 n/a n/a
54 2AOA - S1S C41 H46 N4 O10 c1ccc2c(c1....
55 1TZE ic50 = 148 nM LYS PRO PHE PTR VAL ASN VAL NH2 n/a n/a
56 1CWD - PRO GLU GLY ASP PM3 GLU GLU VAL LEU n/a n/a
57 1LKL Kd = 1540 nM ACE PTR GLU GLU GLY n/a n/a
58 1FBZ - CC1 C30 H41 N3 O10 P2 CC(=O)N[C@....
59 1IJR - CC0 C29 H38 N3 O10 P C[C@@H](c1....
60 1CWE - ACE GLN PM3 GLU GLU ILE PRO n/a n/a
61 5GJI - SER ASP PTR MET ASN MET THR PRO n/a n/a
62 1R1S - ACE PRO ASP PTR GLU ASN LEU n/a n/a
63 1R1P - ACE ASP ASP PTR VAL ASN VAL n/a n/a
64 1R1Q - ACE ARG GLU PTR VAL ASN VAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AYQ; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 AYQ 1 1
2 YVN 0.719512 0.931035
3 AYI 0.674419 0.932203
4 FYQ 0.571429 0.929825
5 YEN 0.5 0.913793
6 TVN 0.434343 0.881356
7 FYI 0.415842 0.866667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4P9Z; Ligand: NMI PTR 02K ASN NH2; Similar sites found with APoc: 44
This union binding pocket(no: 1) in the query (biounit: 4p9z.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZOD HQE None
2 3ZOD FMN None
3 2BVE PH5 None
4 4CS4 ANP None
5 4QVB F42 None
6 5WHT SIA GAL GLC 1.7094
7 4RHS SIA SIA GAL 1.7094
8 5WHT SIA GAL 1.7094
9 3DLG GWE 2.5641
10 4XBA 5GP 2.5641
11 3K87 FAD 2.5641
12 4U03 TLL 3.4188
13 4U03 GTP 3.4188
14 5UBG PRT 3.9823
15 5MW4 5JU 4.2735
16 3BL7 DD1 4.2735
17 1AV5 AP2 4.2735
18 3UDZ ADP 5.12821
19 6FL8 TIY 5.12821
20 6FL8 ADP 5.12821
21 2AWN ADP 5.12821
22 1P7T ACO 5.12821
23 2WET FAD 5.98291
24 4HVA 4HV 5.98291
25 1EU1 GLC 6.83761
26 6F5W KG1 6.83761
27 3N1S 5GP 7.56302
28 5RHN 8BR 8.69565
29 43CA NPO 8.84956
30 3PE2 E1B 10.2564
31 5F1R 42O 10.2564
32 4RVU NDP 10.2564
33 1XOC VAL ASP SER LYS ASN THR SER SER TRP 11.1111
34 4INI AMP 11.1111
35 3NEM AMO 12.8205
36 2FXU BID 13.6752
37 3QWB NDP 13.6752
38 3G6K FAD 13.6752
39 5LIA 6XN 17.094
40 4LO6 SIA GAL 17.094
41 6E8I PTR 17.9487
42 3GXW SIN 27.1845
43 1LCK GLU GLY GLN PTR GLN PRO GLN PRO ALA 45.2991
44 1O44 852 49.0741
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