Receptor
PDB id Resolution Class Description Source Keywords
4D49 2.09 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF COMPUTATIONALLY DESIGNED ARMADILLO REPEAT PROTEINS FOR MODULAR PEPTIDE RECOGNITION. SYNTHETIC CONSTRUCT DE NOVO PROTEIN-PEPTIDE COMPLEX
Ref.: COMPUTATIONALLY DESIGNED ARMADILLO REPEAT PROTEINS MODULAR PEPTIDE RECOGNITION. J.MOL.BIOL. V. 428 4467 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG G:1;
H:2;
C:1;
D:2;
Valid;
Valid;
Invalid;
Valid;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
none;
Atoms found LESS than expected: % Diff = 0;
submit data
1417.8 n/a O=C(N...
ARG D:1011;
E:1011;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
submit data
175.209 C6 H15 N4 O2 C(C[C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5MFI 1.45 Å NON-ENZYME: OTHER DESIGNED ARMADILLO REPEAT PROTEIN YIII(DQ.V2)4CQI IN COMPLEX PEPTIDE (KR)4 SYNTHETIC CONSTRUCT DESIGNED ARMADILLO REPEAT PROTEIN PEPTIDE BINDING DE NOVO DE NOVO PROTEIN
Ref.: CURVATURE OF DESIGNED ARMADILLO REPEAT PROTEINS ALL MODULAR PEPTIDE BINDING. J. STRUCT. BIOL. V. 201 108 2018
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5MFK - LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
2 4D49 - ARG C6 H15 N4 O2 C(C[C@@H](....
3 5MFJ - LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
4 5MFI - LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5MFK - LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
2 4D49 - ARG C6 H15 N4 O2 C(C[C@@H](....
3 5MFJ - LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
4 5MFI - LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
5 5MFE - ARG ARG ARG ARG ARG ARG ARG ARG n/a n/a
6 5MFG - ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG n/a n/a
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 5MFK - LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
2 4D49 - ARG C6 H15 N4 O2 C(C[C@@H](....
3 5MFJ - LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
4 5MFI - LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
5 5MFH - ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG n/a n/a
6 5MFF - ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG n/a n/a
7 5AEI Kd = 1.1 nM LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG n/a n/a
8 5MFE - ARG ARG ARG ARG ARG ARG ARG ARG n/a n/a
9 5MFG - ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 1 1
2 ARG ARG ARG ARG ARG ARG ARG ARG 1 1
3 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.815385 0.97561
4 GLU ALY ARG 0.623377 0.829787
5 ARG ALA ARG 0.621212 0.926829
6 THR ALA ARG M3L SER THR 0.608108 0.689655
7 ARG ARG ALA ALA 0.577465 0.886364
8 BEZ NLE LYS ARG OAR 0.573529 0.925
9 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.571429 0.8125
10 PRO PRO LYS LYS LYS ARG LYS VAL 0.565789 0.886364
11 ARG ASP 0.553846 0.863636
12 LYS ARG LYS 0.541667 0.906977
13 ARG ARG ARG ARG SER TRP TYR 0.532609 0.701754
14 ALA ARG M3L SER 0.531646 0.689655
15 ALA ILE ARG SER 0.518987 0.791667
16 CYS ALA ARG ALA TYR 0.513889 0.860465
17 ARG ARG GLY CYS NH2 0.513514 0.886364
18 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.511905 0.76
19 GLU ARG GLY SER GLY ARG 0.511628 0.816327
20 ARG SER ARG 0.507042 0.829787
21 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.506173 0.886364
22 ARG ASP ALA ALA 0.5 0.844444
23 ARG ARG GLY LEU NH2 0.5 0.847826
24 ARG ARG ARG GLU ARG SER PRO THR ARG 0.495327 0.634921
25 ARG ARG ARG VAL ARG 00S 0.494253 0.833333
26 ARG ARG GLY ILE NH2 0.493506 0.847826
27 ARG LEU GLY GLU SER 0.479452 0.804348
28 GLY ALA ARG 0.478873 0.860465
29 ARG GLU 0.478261 0.883721
30 ALA MET ARG VAL 0.475 0.791667
31 ARG ARG GLY MET NH2 0.475 0.833333
32 ALA ARG THR LYS GLN THR ALA ARG LYS 0.474227 0.8
33 ASN ARG LEU ILE LEU THR GLY 0.47191 0.77551
34 ALA ARG THR LYS GLN THR ALA ARG 0.47191 0.78
35 ARG GLU ALA ALA 0.468354 0.844444
36 ARG GLY ASP 0.466667 0.844444
37 ASN ARG LEU LEU LEU THR GLY 0.464286 0.730769
38 ALA ARG 9AT 0.458333 0.791667
39 ACE THR ARG GLU 0.458333 0.791667
40 ACE ARG LYS VAL ARG MET 5XU 0.45679 0.791667
41 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.456522 0.661017
42 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.455446 0.727273
43 ACE ALA ARG THR LYS GLN 0.449438 0.795918
44 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.448276 0.655738
45 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.447368 0.863636
46 GLU ARG THR ILE PRO ILE THR ARG GLU 0.443396 0.634921
47 ARG ILE ALA ALA ALA 0.44 0.840909
48 ARG ASP ARG ALA ALA LYS LEU 0.436782 0.829787
49 ARG VAL 0.434783 0.822222
50 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.431818 0.722222
51 GLN THR ALA ARG M3L SER 0.431373 0.645161
52 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.43 0.666667
53 LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.428571 0.727273
54 GLU GLU GLU ASP GLY TPO MET LYS ARG ASN 0.427273 0.645161
55 ALA ARG 0.426471 0.860465
56 ARG ARG LEU ILE PHE NH2 0.42268 0.8125
57 ARG ILE PHE SER 0.421053 0.745098
58 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.420168 0.714286
59 VAL ALA PHE ARG SER 0.416667 0.76
60 GLY ARG GLY ASP SER PRO 0.41573 0.791667
61 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.413333 0.673077
62 ARG ARG ALA THR LYS MET NH2 0.41 0.740741
63 LYS ALA ALA ARG M3L SER ALA 0.41 0.666667
64 ACE GLN THR ALA ARG BTK SER THR 0.407767 0.722222
65 DMG PRO ARG ARG ARG SER ARG LYS PRO 0.40625 0.625
66 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.405941 0.769231
67 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.404494 0.8125
68 ARG GLY ARG ALA 2MR GLY GLN GLU 0.40404 0.869565
69 VAL ALA ARG SER 0.402439 0.791667
70 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.402062 0.75
Ligand no: 2; Ligand: ARG; Similar ligands found: 42
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG 1 1
2 DAR 1 1
3 CIR 0.735294 0.763158
4 AAR 0.705882 0.783784
5 ILO 0.615385 0.783784
6 3AR 0.595238 0.891892
7 4JK 0.585366 0.789474
8 NMM 0.585366 0.888889
9 VUR 0.585366 0.810811
10 HAR 0.585366 0.780488
11 VIO 0.581395 0.769231
12 WT2 0.571429 0.805556
13 DA2 0.55814 0.744186
14 2MR 0.545455 0.864865
15 2YH 0.545455 0.65
16 3KJ 0.545455 0.680851
17 1KJ 0.533333 0.744186
18 JM2 0.533333 0.731707
19 NRG 0.521739 0.622642
20 RPI 0.521739 0.64
21 2YJ 0.521739 0.619048
22 API 0.515152 0.611111
23 LN6 0.510638 0.725
24 HRG 0.5 0.941176
25 JM7 0.5 0.731707
26 2KJ 0.489796 0.727273
27 D20 0.489796 0.744186
28 AS1 0.489796 0.8
29 ORN 0.472222 0.757576
30 JM8 0.470588 0.714286
31 JM6 0.470588 0.697674
32 JM4 0.470588 0.697674
33 LYS ARG LYS ARG LYS ARG LYS ARG 0.463415 0.848485
34 MLZ 0.463415 0.65
35 JM5 0.461538 0.714286
36 DLY 0.447368 0.735294
37 DAB 0.441176 0.685714
38 LYS 0.435897 0.764706
39 0TF 0.428571 0.619048
40 2YG 0.42 0.619048
41 PG3 0.416667 0.756757
42 6CL 0.414634 0.638889
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5MFI; Ligand: LYS ARG LYS ARG LYS ARG LYS ARG; 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: 5mfi.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
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