Receptor
PDB id Resolution Class Description Source Keywords
2VDR 2.4 Å NON-ENZYME: OTHER INTEGRIN ALPHAIIBBETA3 HEADPIECE BOUND TO A CHIMERIC FIBRINO CHAIN PEPTIDE, LGGAKQRGDV HOMO SAPIENS CELL ADHESION-IMMUNE SYSTEM COMPLEX FIBRINOGEN BINDING PLAINTEGRIN ALPHAIIBBETA3 GLYCOPROTEIN CELL ADHESION MEMBRAINTEGRIN RECEPTOR ANTAGONIST HOST-VIRUS INTERACTION PYRCARBOXYLIC ACID TRANSMEMBRANE PHOSPHORYLATION DISEASE MUCLEAVAGE ON PAIR OF BASIC RESIDUES
Ref.: STRUCTURAL BASIS FOR DISTINCTIVE RECOGNITION OF FIB GAMMAC PEPTIDE BY THE PLATELET INTEGRIN ALPHAIIBBET J.CELL BIOL. V. 182 791 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:2004;
A:2005;
A:2006;
A:2007;
B:2002;
B:2003;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
 submit data
40.078 Ca [Ca+2...
GOL A:1453;
B:1462;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL C:405;
 Valid;
 none;
 submit data
772.862 n/a O=C([...
MG B:2001;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
NAG A:3015;
A:3249;
B:3099;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG MAN MAN MAN D:1;
 Part of Protein;
 none;
 submit data
910.826 n/a O=C(N...
NAG NAG MAN MAN MAN MAN MAN E:1;
 Part of Protein;
 none;
 submit data
n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ZE2 2.35 Å NON-ENZYME: OTHER INTEGRIN ALPHAIIB BETA3 HEADPIECE AND RGD PEPTIDE COMPLEX HOMO SAPIENS CELL ADHESION-IMMUNE SYSTEM-PEPTIDE COMPLEX CELL ADHESIN-IMSYSTEM-PEPTIDE COMPLEX CELL ADHESION
Ref.: COMPLETE INTEGRIN HEADPIECE OPENING IN EIGHT STEPS. J.CELL BIOL. V. 201 1053 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3NIF - NIF C11 H15 N5 O S CCC1=NN2C(....
2 3ZDY - GLY ARG GLY ASP SER PRO n/a n/a
3 3ZE2 - GLY ARG GLY ASP SER PRO n/a n/a
4 2VDR - LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 3NIF - NIF C11 H15 N5 O S CCC1=NN2C(....
2 3ZDY - GLY ARG GLY ASP SER PRO n/a n/a
3 3ZE2 - GLY ARG GLY ASP SER PRO n/a n/a
4 2VDR - LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL n/a n/a
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3GJF Kd = 46 nM SER LEU LEU MET TRP ILE THR GLN VAL n/a n/a
2 2ZPK - PRO ARG GLY TYR PRO GLY GLN VAL n/a n/a
3 3NIF - NIF C11 H15 N5 O S CCC1=NN2C(....
4 3ZDY - GLY ARG GLY ASP SER PRO n/a n/a
5 3ZE2 - GLY ARG GLY ASP SER PRO n/a n/a
6 2VDR - LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL n/a n/a
7 3WFD - AXO C2 H5 N O C/C=N/O
8 4XTR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 1W72 Kd = 14 nM GLU ALA ASP PRO THR GLY HIS SER TYR n/a n/a
10 6O24 - CIT C6 H8 O7 C(C(=O)O)C....
11 6ID4 Kd = 0.000000064 M ALA ILE PHE GLN SER SER MET THR LYS n/a n/a
12 5X2N - ALA C3 H7 N O2 C[C@@H](C(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 1 1
2 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.520325 0.87037
3 ARG ARG ARG GLU THR GLN VAL 0.514019 0.867925
4 LYS ARG ARG LYS SEP VAL 0.5 0.793103
5 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.5 0.851852
6 ACE LYS ARG ARG LYS SEP VAL 0.495495 0.793103
7 LYS ARG ARG ARG LYS SEP CYS GLN ALA NH2 0.491525 0.75
8 GLY ARG GLY ASP SER PRO 0.490566 0.843137
9 SER SER ARG LYS GLU TYR TYR ALA 0.483051 0.775862
10 ALA ARG LYS LEU ASP 0.471698 0.959184
11 GLY ASP GLU VAL LYS VAL PHE ARG 0.465649 0.941176
12 ALA ASN SER ARG VAL GLN ASP SER ILE ILE 0.459677 0.789474
13 ASP GLN GLY ARG GLY ARG ARG ARG PRO 0.459677 0.75
14 SAC ARG GLY THR GLN THR GLU 0.458333 0.818182
15 THR LYS ASN TYR LYS GLN PHE SER VAL 0.452381 0.634921
16 VAL THR THR ASP ILE GLN VAL LYS VAL 0.45 0.727273
17 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.446809 0.888889
18 LYS ARG LYS 0.444444 0.875
19 GLY GLY LYS LYS ARG TYR LYS LEU 0.443548 0.824561
20 GLY GLY ARG LYS LYS TYR LYS LEU 0.443548 0.824561
21 GLY GLY LYS LYS LYS TYR ARG LEU 0.443548 0.824561
22 GLU ARG GLY MET THR 0.443478 0.785714
23 GLY VAL TYR ASP GLY ARG GLU HIS THR VAL 0.442177 0.712121
24 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.440945 0.746032
25 ALA ARG THR LYS GLN THR ALA ARG LYS 0.434426 0.849057
26 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.433824 0.783333
27 LEU GLU LYS ALA ARG GLY SER THR TYR 0.431507 0.786885
28 PAC DLY DLY DAR 0.431193 0.862745
29 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.429907 0.826923
30 ALA ASN GLY GLY ALA SER GLY GLN VAL LYS 0.429688 0.745455
31 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.426087 0.882353
32 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.425676 0.758065
33 ALA VAL TYR ASP GLY ARG GLU HIS THR VAL 0.425676 0.712121
34 LEU TYR LEU VAL CYS GLY GLU ARG VAL 0.425532 0.762712
35 SER ASP TYR GLN ARG LEU 0.425 0.789474
36 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.422764 0.867925
37 GLY ALA ASP GLY VAL GLY LYS SER ALA 0.421488 0.759259
38 ILE GLN GLN SER ILE GLU ARG ILE 0.421488 0.833333
39 THR ILE MET MET GLN ARG GLY 0.421488 0.793103
40 HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.42069 0.783333
41 THR ASN GLU TYR LYS VAL 0.420168 0.689655
42 LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.41958 0.79661
43 ALA ARG LYS ILE ASP ASN LEU ASP 0.418605 0.87037
44 GLU GLU GLU ASP GLY TPO MET LYS ARG ASN 0.41791 0.746032
45 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.417266 0.783333
46 SER ARG LYS ILE ASP ASN LEU ASP 0.416667 0.824561
47 THR ARG ARG GLU THR GLN LEU 0.415254 0.851852
48 ARG LYS LYS ARG TYR THR VAL VAL GLY ASN 0.414286 0.783333
49 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.413793 0.712121
50 ARG ARG GLY ILE NH2 0.413462 0.823529
51 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.412698 0.810345
52 ALA ARG THR MLY GLN 0.410256 0.783333
53 LYS ARG GLU ALA ILE VAL LYS ALA ASP GLU 0.409836 0.82
54 GLU GLN TYR LYS PHE TYR SER VAL 0.407692 0.672131
55 ARG GLY TYR VAL TYR GLN GLY LEU 0.407407 0.762712
56 ALA ARG THR LYS GLN THR ALA ARG 0.405172 0.865385
57 ALA LYS PHE ARG HIS ASP 0.40458 0.762712
58 ARG ARG GLY LEU NH2 0.403846 0.86
59 ALA ARG TPO LYS 0.403509 0.775862
60 ALA ARG THR M3L GLN THR ALA ARG 0.403226 0.746032
61 GLY GLY LYS LYS LYS TYR GLN LEU 0.403226 0.719298
62 ARG GLY ASP ILE ASN ASN ASN VAL 0.403226 0.851852
63 PRO VAL LYS ARG ARG LEU ASP LEU GLU 0.40146 0.872727
64 ALA ARG THR ALY GLN THR ALA 0.4 0.818182
Similar Ligands (3D)
Ligand no: 1; Ligand: LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL; 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 : 3ZE2; Ligand: GLY ARG GLY ASP SER PRO; 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: 3ze2.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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