Receptor
PDB id Resolution Class Description Source Keywords
1BMB 1.8 Å NON-ENZYME: SIGNAL_HORMONE GRB2-SH2 DOMAIN IN COMPLEX WITH KPFY*VNVEF (PKF270-974) HOMO SAPIENS SH2 DOMAIN SIGNAL TRANSDUCTION ADAPTOR PROTEIN RAS PATHWAY HORMONE/GROWTH FACTOR COMPLEX
Ref.: STRUCTURAL AND CONFORMATIONAL REQUIREMENTS FOR HIGH-AFFINITY BINDING TO THE SH2 DOMAIN OF GRB2(1). J.MED.CHEM. V. 42 971 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LYS PRO PHE PTR VAL ASN VAL GLU PHE I:1;
Valid;
none;
ic50 = 0.7 uM
1220.29 n/a P(=O)...
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 301 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 (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 221 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 3IMD Ka = 560000 M^-1 FYQ C21 H31 N6 O10 P CNC(=O)C[C....
8 3N84 - PTR VAL ASN VAL PRO 011 n/a n/a
9 3MXY Kd = 384 nM GLN ASN GLY PTR VAL ASN PRO THR TYR n/a n/a
10 1JYQ Kd = 2.5 nM MAZ PTR PTM ASN n/a n/a
11 2AOA - S1S C41 H46 N4 O10 c1ccc2c(c1....
12 1TZE ic50 = 148 nM LYS PRO PHE PTR VAL ASN VAL NH2 n/a n/a
50% Homology Family (65)
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 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 PRO 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 5GJH - SER ASP PTR MET ASN MET THR PRO n/a n/a
63 1R1S - ACE PRO ASP PTR GLU ASN LEU n/a n/a
64 1R1P - ACE ASP ASP PTR VAL ASN VAL n/a n/a
65 1R1Q - ACE ARG GLU PTR VAL ASN VAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LYS PRO PHE PTR VAL ASN VAL GLU PHE; Similar ligands found: 121
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS PRO PHE PTR VAL ASN VAL GLU PHE 1 1
2 LYS PRO PHE PTR VAL ASN VAL NH2 0.843284 0.985915
3 LYS PRO ILE VAL GLN TYR ASP ASN PHE 0.660256 0.864865
4 ALA PRO SER PTR VAL ASN VAL GLN ASN 0.648649 0.906667
5 LEU PRO PHE GLU LYS SER THR VAL MET 0.554878 0.734177
6 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.552795 0.739726
7 ACE PRO ASP PTR GLU ASN LEU 0.550336 0.905405
8 GLN ASN GLY PTR VAL ASN PRO THR TYR 0.534591 0.958904
9 6NA PTR VAL ASN VAL 9PR 0.532895 0.881579
10 GLY GLN VAL PRO PHE SER LYS GLU GLU CYS 0.530864 0.75
11 PRO GLN PTR GLU PTR ILE PRO ALA 0.52795 0.917808
12 GLU VAL PTR GLU SER PRO 0.526667 0.891892
13 GLN ASN GLY PTR GLU ASN PRO THR TYR 0.525 0.90411
14 PRO GLN PTR GLU GLU ILE PRO ILE 0.521739 0.890411
15 SER PTR VAL ASN VAL GLN ASN 0.506849 0.743243
16 TYR PRO ASN VAL ASN ILE HIS ASN PHE 0.5 0.828947
17 ASP PHE GLU GLU ILE PRO GLY GLU PTR 0.49711 0.931507
18 PHE PRO THR LYS ASP VAL ALA LEU 0.49697 0.783784
19 ACE ARG GLU PTR VAL ASN VAL 0.493506 0.74026
20 ILE THR ASP GLN VAL PRO PHE SER VAL 0.491018 0.75
21 LEU PRO SER PHE GLU THR ALA LEU 0.490683 0.76
22 PRO GLN PTR ILE PTR VAL PRO ALA 0.487805 0.931507
23 SER PHE PHE GLU ASP ASN PHE VAL PRO GLU 0.484076 0.810811
24 LEU PRO PHE GLU ARG ALA THR VAL MET 0.483146 0.698795
25 LYS LEU PRO ALA GLN PHE TYR ILE LEU 0.482759 0.810811
26 GLY TYR GLU ASN PRO THR TYR LYS PHE PHE 0.482759 0.849315
27 SER THR SEP PRO THR PHE ASN LYS 0.482558 0.864865
28 GLU GLY GLN PTR GLN PRO GLN PRO ALA 0.481928 0.901408
29 DHI PRO PHE HIS LEU LEU VAL TYR 0.477012 0.786667
30 LEU PRO PHE ASP LYS THR THR ILE MET 0.476744 0.734177
31 LEU PRO PHE ASP LYS SER THR ILE MET 0.474576 0.725
32 GLU ILE ILE ASN PHE GLU LYS LEU 0.467949 0.630137
33 ARG VAL ILE PTR PHE VAL PRO LEU ASN ARG 0.467532 0.876712
34 LYS THR PHE PRO PRO THR GLU PRO LYS 0.467066 0.794521
35 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.463415 0.636364
36 ALA GLY SER VAL GLU GLN TPO PRO LYS LYS 0.462428 0.84
37 ASP PHE GLU GLU ILE PRO GLU GLU TYS 0.461538 0.804878
38 SER ASP PTR MET ASN MET THR PRO 0.461078 0.848101
39 GLY SER ASP PRO PHE LYS 0.460526 0.72973
40 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.45977 0.849315
41 PTR VAL PRO MET LEU 0.458599 0.828947
42 ACE ASP ASP PTR VAL ASN VAL 0.458333 0.708333
43 LYS PRO ILE VAL VAL LEU HIS GLY TYR 0.458101 0.789474
44 GLU GLU PRO THR VAL ILE LYS LYS TYR 0.456647 0.8
45 SER ILE ILE ASN PHE GLU LYS LEU 0.455696 0.605263
46 ILE MET ASP GLN VAL PRO PHE SER VAL 0.454023 0.7
47 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 0.454023 0.810811
48 ACE PTR VAL ASN VAL 0.453237 0.708333
49 LEU GLN ARG VAL LEU SEP ALA PRO PHE 0.452941 0.7625
50 ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.451613 0.833333
51 THR PRO TYR ASP ILE ASN GLN MET LEU 0.451429 0.759494
52 SER ILE TYR PHE TPO PRO GLU LEU TYR ASP 0.451087 0.907895
53 TRP GLU TYR ILE PRO ASN VAL 0.449438 0.815789
54 ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU 0.449438 0.829268
55 ACE LEU TYR ALA SER SER ASN PRO ALA PTR 0.447674 0.921053
56 ARG PRO MET THR PHE LYS GLY ALA LEU 0.446237 0.690476
57 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.443787 0.794521
58 ALA PRO GLN PRO ALA PRO GLU ASN ALA TYR 0.443114 0.821918
59 PHE GLU ALA ILE PRO ALA GLU TYR LEU 0.44186 0.783784
60 PHE ASN PHE PRO GLN ILE THR 0.441718 0.773333
61 GLU PRO VAL GLU THR THR ASP TYR 0.438272 0.794521
62 LEU PRO PHE GLU ARG ALA THR ILE MET 0.437838 0.690476
63 1IP CYS PHE SER LYS PRO ARG 0.436782 0.703704
64 ARG PRO PRO ILE PHE ILE ARG ARG LEU 0.436047 0.717949
65 LYS LEU TYR GLN ASN PRO THR THR TYR ILE 0.435754 0.84
66 TYR MET PHE PRO ASN ALA PRO TYR LEU 0.434286 0.807692
67 SER PRO ILE VAL PRO SER PHE ASP MET 0.433526 0.725
68 ASN ASP LYS TYR GLU PRO PHE TRP GLU 0.430052 0.824324
69 VAL ORN LEU DPN PRO VAL ORN LEU DPN PRO 0.429448 0.763889
70 LEU TYR ALA SER PRO GLN LEU GLU GLY PHE 0.428571 0.8
71 GLU ASN GLN LYS GLU TYR PHE PHE 0.427632 0.680556
72 TYR MET ASP PHE ASP ASP ASP ILE PRO PHE 0.427536 0.671233
73 LYS VAL PRO ARG ASN GLN ASP TRP LEU 0.427083 0.772152
74 LYS MET ASN THR GLN PHE THR ALA VAL 0.42515 0.615385
75 MAA LPH PRO PHE 4LZ 0.424419 0.7625
76 LYS PRO HIS SER ASP 0.424051 0.723684
77 ARG SEP PRO VAL PHE SER 0.421965 0.759494
78 PHE LEU PRO SER ASP PHE PHE PRO SER VAL 0.421687 0.8
79 PHE SER ALA PTR PRO SER GLU GLU ASP 0.421687 0.878378
80 THR LYS ASN TYR LYS GLN PHE SER VAL 0.421384 0.702703
81 LEU SER SER PRO VAL THR LYS SER PHE 0.421053 0.746667
82 ARG MET PHE PRO ASN ALA PRO TYR LEU 0.419355 0.783133
83 TRP MET ASP PHE ASP ASP ASP ILE PRO PHE 0.418919 0.712329
84 TRP ASP ILE PRO PHE 0.418919 0.712329
85 ASP GLU PTR GLU ASN VAL ASP 0.418301 0.760563
86 ASP ARG VAL GLU LEU ASN ALA PRO ARG GLN 0.417647 0.717949
87 ASP ILE ASN TYS TYS THR SER GLU PRO 0.417647 0.8
88 ALA CYS SEP PRO GLN PHE GLY 0.416667 0.810811
89 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.416667 0.643836
90 PHE ASN ARG PRO VAL 0.416149 0.75
91 LEU PRO PHE ASP ARG THR THR ILE MET 0.415301 0.702381
92 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.414894 0.725
93 GLU LEU PRO LEU VAL LYS ILE 0.41358 0.712329
94 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.412088 0.734177
95 ARG THR TYR SEP GLY PRO MET ASN LYS VAL 0.41206 0.821429
96 LEU ASN PHE PRO ILE SER PRO 0.409938 0.776316
97 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.409836 0.824324
98 PRO LYS ARG PRO THR THR LEU ASN LEU PHE 0.407407 0.759494
99 LYS PRO VAL LEU ARG THR ALA 0.407186 0.696203
100 PHE TYR ALA PRO GLU PRO ILE THR SER LEU 0.406593 0.818182
101 ARG PRO MET THR TYR LYS GLY ALA LEU 0.40625 0.72619
102 LEU PRO PRO VAL VAL ALA LYS GLU ILE 0.405882 0.739726
103 GLN MET PRO THR GLU ASP GLU TYR 0.405714 0.75641
104 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.405128 0.722892
105 GLU VAL ALA PRO PRO GLU TYR HIS ARG LYS 0.405 0.78481
106 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.404494 0.786667
107 SEP GLN GLU PTR 0.40411 0.684932
108 CYS THR GLU LEU LYS LEU ASN ASP TYR 0.403614 0.666667
109 LYS ALA VAL PHE ASN PHE ALA THR MET 0.403614 0.628205
110 LEU PHE GLY TYR PRO VAL TYR VAL 0.403509 0.808219
111 LYS PRO SEP GLN GLU LEU 0.402597 0.786667
112 TYR PRO TYR ASP VAL PRO ASP TYR ALA 0.402439 0.847222
113 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.402116 0.820513
114 LYS VAL ILE THR PHE ILE ASP LEU 0.401235 0.613333
115 LYS ALA VAL TYR ASN PHE ALA THR MET 0.401163 0.666667
116 ALA PHE ARG ILE PRO LEU THR ARG 0.40113 0.725
117 GLU SER ASP PRO ILE VAL ALA GLN TYR 0.4 0.789474
118 ACE GLU VAL ASN ALA PRO VAL LPD 0.4 0.777778
119 ARG GLN PHE GLY PRO ASP PHE PRO THR ILE 0.4 0.7625
120 LYS VAL LEU PHE LEU ASP GLY 0.4 0.611111
121 LYS PRO LYS 0.4 0.661972
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: 1
This union binding pocket(no: 1) in the query (biounit: 4p9z.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1LCK GLU GLY GLN PTR GLN PRO GLN PRO ALA 45.2991
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