Receptor
PDB id Resolution Class Description Source Keywords
3c7i 1.7 Å NON-ENZYME: SIGNAL_HORMONE X-RAY CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE GRB2-SH2 DOMAIN AND A FLEXIBLE LIGAND, FPTVN. HOMO SAPIENS FLEXIBLE CONSTRAINED ENTROPY GRB2-SH2 LIGAND PREORGANIZATION ALTERNATIVE SPLICING HOST-VIRUS INTERACTION PHOSPHOPROTEIN SH2 DOMAIN SH3 DOMAIN
Ref.: LIGAND PREORGANIZATION MAY BE ACCOMPANIED BY ENTROPIC PENALTIES IN PROTEIN-LIGAND INTERACTIONS. ANGEW.CHEM.INT.ED.ENGL. V. 118 6984 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMT A:201;
 Invalid;
 none;
 submit data
46.025 C H2 O2 C(=O)...
TVN A:202;
 Valid;
 none;
 Ka = 440000 M^-1
529.481 C21 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 (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3C7I Ka = 440000 M^-1 TVN C21 H32 N5 O9 P CC(C)[C@@H....
2 3S8O Ka = 6960000 M^-1 ACE PTR 02K ASN NH2 n/a n/a
3 1O48 ic50 = 450 nM 853 C33 H35 N3 O7 CC(=O)N[C@....
4 1O4N ic50 > 40 mM OXD C2 H2 O4 C(=O)(C(=O....
5 1O44 ic50 = 3 nM 852 C34 H35 N3 O9 CC(=O)N[C@....
6 1O4G ic50 > 5 mM I59 C11 H11 O4 P c1ccc2c(c1....
7 1SHD ic50 = 0.67 uM ACE PTR GLU GLU ILE GLU n/a n/a
8 1O4O ic50 = 3.5 mM HPS C6 H7 O4 P c1ccc(cc1)....
9 1A08 Kd = 2.4 uM ACE FTY GLU DIP n/a n/a
10 1A07 Kd = 0.4 uM ACE PTR GLU DIP n/a n/a
11 1JYQ Kd = 2 nM MAZ PTR PTM ASN n/a n/a
12 1LKK Kd = 140 nM ACE PTR GLU GLU ILE ACE n/a n/a
13 1BHF Kd = 42 uM ACE 1PA GLU GLU ILE n/a n/a
14 1LCK - GLU GLY GLN PTR GLN PRO GLN PRO ALA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TVN; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 TVN 1 1
2 FYI 0.831169 0.947368
3 FYQ 0.698795 0.946429
4 YEN 0.690476 0.929825
5 YVN 0.561798 0.913793
6 AYI 0.494737 0.883333
7 AYQ 0.434343 0.881356
Similar Ligands (3D)
Ligand no: 1; Ligand: TVN; Similar ligands found: 5
No: Ligand Similarity coefficient
1 ACT PTR 1AC ASN NH2 0.9093
2 ACE PTR 192 ASN NH2 0.9077
3 ACE PTR AC5 ASN NH2 0.9062
4 ACE PTR 02K ASN NH2 0.8932
5 ACT PTR 03E ASN NH2 0.8755
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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