Receptor
PDB id Resolution Class Description Source Keywords
1TZE 2.1 Å NON-ENZYME: SIGNAL_HORMONE SIGNAL TRANSDUCTION ADAPTOR GROWTH FACTOR, GRB2 SH2 DOMAIN C WITH PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-V( KFPPYVNC-NH2) HOMO SAPIENS SIGNAL TRANSDUCTION ADAPTOR GROWTH FACTOR BOUND PROTEIN 2 (GHOMOLOGY 2 DOMAIN (SH2) PHOSPHOTYROSYL HEPTAPEPTIC LIGAND(SIGNAL TRANSDUCTION-PEPTIDE) COMPLEX (SIGNAL TRANSDUCTIONCOMPLEX
Ref.: STRUCTURAL BASIS FOR SPECIFICITY OF GRB2-SH2 REVEAL NOVEL LIGAND BINDING MODE. NAT.STRUCT.BIOL. V. 3 586 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LYS PRO PHE PTR VAL ASN VAL NH2 I:1;
Valid;
none;
ic50 = 0.148 uM
946.033 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1JYQ 2 Å NON-ENZYME: SIGNAL_HORMONE XRAY STRUCTURE OF GRB2 SH2 DOMAIN COMPLEXED WITH A HIGHLY AF PHOSPHO PEPTIDE HOMO SAPIENS RECEPTOR BINDING REGULATORY SIGNALING PROTEIN-SIGNALING PRINHIBITOR SIGNALING PROTEIN-PEPTIDE INHIBITOR COMPLEX
Ref.: CRYSTAL STRUCTURES OF THE SH2 DOMAIN OF GRB2: HIGHL THE BINDING OF A NEW HIGH-AFFINITY INHIBITOR. J.MOL.BIOL. V. 315 1167 2002
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 3MXY Kd = 384.8 nM GLN ASN GLY PTR VAL ASN PRO THR TYR n/a n/a
2 1JYQ Kd = 2 nM MAZ PTR PTM ASN n/a n/a
3 3WA4 - SER ASP PTR MET ASN MET THR PRO n/a n/a
4 3MXC Kd = 286.1 nM GLN ASN GLY PTR GLU ASN PRO THR TYR n/a n/a
5 3N7Y Ka = 10000000 M^-1 PTR VAL ASN VAL 011 n/a n/a
6 2AOB - S1S C41 H46 N4 O10 c1ccc2c(c1....
7 1JYR Kd = 18 nM ALA PRO SER PTR VAL ASN VAL GLN ASN n/a n/a
8 1ZFP ic50 = 26 nM BE2 GLU PTR ILE ASN GLN NH2 n/a n/a
9 2AOA - S1S C41 H46 N4 O10 c1ccc2c(c1....
10 1TZE ic50 = 0.148 uM LYS PRO PHE PTR VAL ASN VAL NH2 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: LYS PRO PHE PTR VAL ASN VAL NH2; Similar ligands found: 108
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS PRO PHE PTR VAL ASN VAL NH2 1 1
2 LYS PRO PHE PTR VAL ASN VAL GLU PHE 0.843284 0.985915
3 ALA PRO SER PTR VAL ASN VAL GLN ASN 0.615385 0.893333
4 LYS PRO ILE VAL GLN TYR ASP ASN PHE 0.576923 0.851351
5 6NA PTR VAL ASN VAL 9PR 0.571429 0.893333
6 SER THR SEP PRO THR PHE ASN LYS 0.531646 0.876712
7 ASP TYR ASN PRO TYR LEU LEU PHE LEU LYS 0.509804 0.863014
8 GLN ASN GLY PTR VAL ASN PRO THR TYR 0.506579 0.945205
9 ARG VAL ILE PTR PHE VAL PRO LEU ASN ARG 0.503546 0.888889
10 LEU PRO PHE GLU LYS SER THR VAL MET 0.484663 0.721519
11 TYR PRO ASN VAL ASN ILE HIS ASN PHE 0.47561 0.815789
12 ILE THR ASP GLN VAL PRO PHE SER VAL 0.475 0.736842
13 ARG SEP PRO VAL PHE SER 0.474684 0.769231
14 PHE PRO THR LYS ASP VAL ALA LEU 0.471698 0.77027
15 PRO GLN PTR ILE PTR VAL PRO ALA 0.471338 0.917808
16 LEU PRO PHE ASP LYS THR THR ILE MET 0.469512 0.721519
17 GLU VAL PTR GLU SER PRO 0.469388 0.878378
18 SER PTR VAL ASN VAL GLN ASN 0.468085 0.72973
19 PHE SER ALA PTR PRO SER GLU GLU ASP 0.467105 0.890411
20 ASP PHE GLU GLU ILE PRO GLY GLU PTR 0.464286 0.917808
21 SER ASP PTR MET ASN MET THR PRO 0.462025 0.835443
22 GLY SER ASP PRO PHE LYS 0.461538 0.716216
23 DHI PRO PHE HIS LEU LEU VAL TYR 0.461078 0.773333
24 GLY GLN VAL PRO PHE SER LYS GLU GLU CYS 0.459627 0.736842
25 LYS PRO ILE VAL VAL LEU HIS GLY TYR 0.458824 0.776316
26 LEU PRO PHE ASP LYS SER THR ILE MET 0.458824 0.7125
27 LYS LEU PRO ALA GLN PHE TYR ILE LEU 0.458333 0.797297
28 PRO GLN PTR GLU PTR ILE PRO ALA 0.45625 0.90411
29 GLU GLY GLN PTR GLN PRO GLN PRO ALA 0.45625 0.887324
30 ALA THR PRO PHE GLN GLU 0.455782 0.712329
31 ARG PRO MET THR PHE LYS GLY ALA LEU 0.454545 0.678571
32 THR THR ALA PRO PHE LEU SER GLY LYS 0.453988 0.75
33 1IP CYS PHE SER LYS PRO ARG 0.453988 0.691358
34 PRO GLN PTR GLU GLU ILE PRO ILE 0.45 0.876712
35 PTR VAL PRO MET LEU 0.449664 0.815789
36 TYR PRO PHE PHE NH2 0.447761 0.746479
37 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.445122 0.726027
38 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.44375 0.780822
39 PHE ASN PHE PRO GLN ILE THR 0.441558 0.76
40 GLY TYR GLU ASN PRO THR TYR LYS PHE PHE 0.441176 0.835616
41 DPN PRO DAR DTH NH2 0.440559 0.688312
42 GLN ASN GLY PTR GLU ASN PRO THR TYR 0.440252 0.890411
43 VAL ORN LEU DPN PRO VAL ORN LEU DPN PRO 0.437909 0.774648
44 ACE ASP PTR ALA GLU PRO MET ASP ALA NH2 0.436364 0.818182
45 LEU ASN PHE PRO ILE SER PRO 0.436242 0.763158
46 LYS LEU TYR GLN ASN PRO THR THR TYR ILE 0.435294 0.851351
47 PHE ASN ARG PRO VAL 0.433333 0.736842
48 ALA CYS SEP PRO GLN PHE GLY 0.433121 0.821918
49 SER PRO ILE VAL PRO SER PHE ASP MET 0.432927 0.7125
50 PHE SER ALA PTR VAL SER GLU GLU ASP 0.431507 0.712329
51 DPN PRO DAR ILE NH2 0.430556 0.649351
52 PHE LEU PRO SER ASP PHE PHE PRO SER VAL 0.429487 0.786667
53 PRO LYS ARG PRO THR THR LEU ASN LEU PHE 0.429379 0.769231
54 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.429379 0.734177
55 SER PHE PHE GLU ASP ASN PHE VAL PRO GLU 0.428571 0.797297
56 ILE MET ASP GLN VAL PRO PHE SER VAL 0.428571 0.6875
57 LEU SER SER PRO VAL THR LYS SER PHE 0.428571 0.756757
58 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.427711 0.773333
59 LEU PRO SER PHE GLU THR ALA LEU 0.427673 0.746667
60 LEU PHE GLY TYR PRO VAL TYR VAL 0.427673 0.794521
61 ASP ASP LEU ASP VAL PRO SER PHE LEU GLN 0.427673 0.746667
62 ARG PRO PRO ILE PHE ILE ARG ARG LEU 0.426829 0.705128
63 LEU PRO PHE GLU ARG ALA THR VAL MET 0.426136 0.686747
64 TYR MET PHE PRO ASN ALA PRO TYR LEU 0.42515 0.794872
65 PHE GLU ASP ASN PHE VAL PRO 0.423841 0.830986
66 LYS THR PHE PRO PRO THR GLU PRO LYS 0.423313 0.780822
67 ASP PHE ALA ASN THR PHE LEU PRO 0.423077 0.797297
68 LYS PRO VAL LEU ARG THR ALA 0.423077 0.683544
69 LYS PRO HIS SER ASP 0.422819 0.710526
70 GLN LEU SER PRO PHE PRO PHE ASP LEU 0.42236 0.773333
71 ACE LEU TYR ALA SER SER ASN PRO ALA PTR 0.421687 0.907895
72 ASP TYR ILE ASN THR ASN VAL LEU PRO 0.421384 0.786667
73 LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.420732 0.794521
74 LEU LEU PHE GLY TYR PRO VAL TYR VAL 0.420732 0.794521
75 ACE GLY LYS SER PHE SER LYS PRO ARG 0.420382 0.723684
76 SER ILE TYR PHE TPO PRO GLU LEU TYR ASP 0.418994 0.894737
77 TYR PRO TYR ASP VAL PRO ASP TYR ALA 0.418301 0.833333
78 LEU GLN ARG VAL LEU SEP ALA PRO PHE 0.418182 0.75
79 ASP PHE GLU GLU ILE PRO GLU GLU TYS 0.418182 0.792683
80 ARG MET PHE PRO ASN ALA PRO TYR LEU 0.418079 0.771084
81 ARG THR TYR SEP GLY PRO MET ASN LYS VAL 0.417989 0.809524
82 ACE GLY ASN CYS PHE SER LYS PRO ARG 0.417722 0.733333
83 THR PRO TYR ASP ILE ASN GLN MET LEU 0.417647 0.746835
84 ALA PHE ARG ILE PRO LEU THR ARG 0.415663 0.7125
85 MAA LYS PRO PHE 0.415493 0.704225
86 PHE SER HIS PRO GLN ASN THR 0.414634 0.763158
87 PHE CYS HIS PRO GLN ASN THR NH2 0.414634 0.773333
88 LEU PRO PHE ASP ARG THR THR ILE MET 0.413793 0.690476
89 ARG PRO MET THR TYR LYS GLY ALA LEU 0.412088 0.714286
90 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.409357 0.835616
91 GLY ASP CYS PHE SER LYS PRO ARG 0.408284 0.675
92 LYS PRO LYS 0.408 0.647887
93 ALA VAL ALA PHE TYR ILE PRO ASP GLN ALA 0.407895 0.767123
94 ASN ASP LYS TYR GLU PRO PHE TRP GLU 0.406417 0.810811
95 ALA LEU MET PRO GLY GLN PHE PHE VAL 0.406061 0.710526
96 GLN VAL ASN PHE LEU GLY LYS 0.405229 0.638889
97 ARG THR PHE SER PRO THR TYR GLY LEU 0.404624 0.775
98 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.404624 0.703704
99 ALA GLY SER VAL GLU GLN TPO PRO LYS LYS 0.403509 0.826667
100 LYS VAL PRO ARG ASN GLN ASP TRP LEU 0.403226 0.759494
101 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.403226 0.710843
102 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.402367 0.730769
103 ASP GLY PTR MET PRO 0.401316 0.828947
104 BOC HIS PRO PHE HIS STA LEU PHE 0.401198 0.782051
105 ACE GLU HIS PHE ILE VAL PRO ASP LEU TYR 0.4 0.746667
106 PHE LYS TPO GLU GLY PRO ASP SER ASP 0.4 0.847222
107 DPN PRO DAR CYS NH2 0.4 0.644737
108 LEU PRO PHE GLU LEU ARG GLY HIS LEU VAL 0.4 0.730769
Similar Ligands (3D)
Ligand no: 1; Ligand: LYS PRO PHE PTR VAL ASN VAL NH2; 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 : 1JYQ; Ligand: MAZ PTR PTM ASN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1jyq.bio2) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1JYQ; Ligand: MAZ PTR PTM ASN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1jyq.bio2) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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