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Receptor
PDB id Resolution Class Description Source Keywords
2B1N 2.4 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF A PAPAIN-FOLD PROTEIN WITHOUT THE CATAL CYSTEINE FROM SEEDS OF PACHYRHIZUS EROSUS PACHYRHIZUS EROSUS PAPAIN-LIKE PEPTIDE FRAGMENT SUGAR BINDING PROTEIN
Ref.: CRYSTAL STRUCTURE OF A PAPAIN-FOLD PROTEIN WITHOUT CATALYTIC RESIDUE: A NOVEL MEMBER IN THE CYSTEINE P FAMILY J.MOL.BIOL. V. 358 97 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LYS ALA SER VAL GLY B:1;
Valid;
none;
submit data
461.54 n/a O=C(N...
NAG FUC NAG A:600;
Invalid;
none;
submit data n/a n/a n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2B1N 2.4 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF A PAPAIN-FOLD PROTEIN WITHOUT THE CATAL CYSTEINE FROM SEEDS OF PACHYRHIZUS EROSUS PACHYRHIZUS EROSUS PAPAIN-LIKE PEPTIDE FRAGMENT SUGAR BINDING PROTEIN
Ref.: CRYSTAL STRUCTURE OF A PAPAIN-FOLD PROTEIN WITHOUT CATALYTIC RESIDUE: A NOVEL MEMBER IN THE CYSTEINE P FAMILY J.MOL.BIOL. V. 358 97 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 2B1N - LYS ALA SER VAL GLY n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 2B1N - LYS ALA SER VAL GLY n/a n/a
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 6EX8 Ki = 11 nM C2K C25 H27 Cl F3 N3 O4 c1cc2c(cc1....
2 6EXO Ki = 5.1 nM C3E C24 H22 Cl N3 O4 c1ccc2c(c1....
3 6EXQ Ki = 9 nM C2W C25 H26 Cl N3 O5 COc1ccc2c(....
4 1PIP Ki < 10 uM SIN GLN VAL VAL ALA ALA NIT n/a n/a
5 1BQI - SBA C22 H36 N2 O5 CC(C)C[C@@....
6 2B1N - LYS ALA SER VAL GLY n/a n/a
7 3H8C Ki = 0.019 uM NSZ C41 H49 N7 O4 S [H]/N=C(/N....
8 3K24 - GLN LEU ALA n/a n/a
9 3H89 Ki = 0.023 uM NSX C57 H64 N8 O6 [H]/N=C(N)....
10 6F06 - C7T C27 H27 Cl N4 O4 c1cc2c(cc1....
11 3BC3 Ki = 0.155 uM OPT C47 H55 N7 O5 S c1ccc(cc1)....
12 3H8B Ki = 0.511 uM NSY C57 H64 N8 O5 [H]/N=C(N)....
13 2HH5 Ki = 32 nM GNQ C25 H31 F3 N4 O6 S C[C@@H](CN....
14 2HHN Ki = 32 nM GNQ C25 H31 F3 N4 O6 S C[C@@H](CN....
15 4P6E ic50 = 1290 nM 2FC C23 H28 N4 O2 CN1CCN(CC1....
16 5QBV - N2D C34 H34 Cl2 N6 O3 CN1c2ccc(c....
17 3IEJ ic50 = 0.22 uM 599 C29 H30 Cl2 N4 O3 c1cc(ccc1C....
18 4P6G ic50 = 7.7 nM 2FZ C25 H29 F N4 O5 CNC(=O)O[C....
19 5QBY - N2A C34 H33 Cl2 F N6 O3 CN1c2ccc(c....
20 5QC4 ic50 = 0.15 uM BC7 C32 H44 F3 N5 O4 S CC(=O)N1CC....
21 2F1G Ki = 0.029 uM GNF C25 H32 N4 O3 COc1ccc(cc....
22 2ATO Ki = 0.6 uM MYQ C4 H5 Au O4 S C([C@@H](C....
23 4X6H Ki = 22 nM I37 C16 H19 F N4 O2 c1cc(c(cc1....
24 4X6I Ki = 10 nM 3Y1 C16 H19 Br N4 O2 c1cc(c(cc1....
25 5JA7 - 6HM C16 H14 O4 c1ccc(cc1)....
26 1Q6K ic50 = 100 nM TCO C13 H23 N O3 CC(C)(C)OC....
27 3KX1 ic50 = 100 nM KX1 C20 H30 N4 c1c(nc(nc1....
28 5J94 - 1XF C10 H10 N2 O4 S c1ccc(c(c1....
29 3C9E Kd = 14 nM BDP ASG BDP ASG BDP ASG n/a n/a
30 4N8W - ASG C8 H15 N O9 S CC(=O)N[C@....
31 1U9Q Ki = 1102.9 nM 186 C23 H24 N2 O5 C[C@@H](C=....
32 3KKU Ki = 2 uM B95 C17 H16 Br N3 O2 c1ccc2c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LYS ALA SER VAL GLY; Similar ligands found: 24
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS ALA SER VAL GLY 1 1
2 LYS ALA LYS 0.542857 0.8
3 VAL THR SER VAL VAL 0.506849 0.863636
4 LYS SER ALA TPO THR THR VAL MET ASN PRO 0.505376 0.777778
5 LYS SER LYS 0.479452 0.888889
6 LYS VAL LYS 0.466667 0.844444
7 GLY THR LEU SER ASN ARG ALA SER LYS LEU 0.458824 0.955556
8 LYS LYS LYS ALA 0.447368 0.8
9 LYS ALA ALA ARG M3L SER ALA 0.436893 0.677419
10 PHE GLU ALA LYS LYS LEU VAL 0.430233 0.826087
11 ILE LEU SER ALA LEU VAL GLY ILE VAL 0.42 0.891304
12 ARG ASP ARG ALA ALA LYS LEU 0.419355 0.730769
13 LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.419048 0.916667
14 LYS LEU VAL GLN LEU LEU THR THR THR 0.418367 0.914894
15 LYS THR LYS 0.417722 0.869565
16 LYS CYS VAL VAL MET 0.41573 0.795918
17 ALA ALA ALA ALA SER ALA ALA 0.413333 0.840909
18 ALA LYS ALA SER GLN ALA ALA 0.408602 0.954545
19 ASP GLU VAL THR SER THR THR SER SER SER 0.406977 0.826087
20 ILE LEU SER ALA LEU VAL GLY ILE LEU 0.405941 0.891304
21 LYS VAL LEU PHE LEU ASP GLY 0.40566 0.816327
22 LYS LEU LYS 0.405063 0.826087
23 LYS THR LYS LEU LEU 0.4 0.893617
24 LYS LYS LYS 0.4 0.777778
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2B1N; Ligand: LYS ALA SER VAL GLY; Similar sites found with APoc: 87
This union binding pocket(no: 1) in the query (biounit: 2b1n.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1P0F NAP 1.62602
2 2DUR MAN MAN 1.62602
3 5FFF NAP 2.03252
4 3HB5 NAP 2.03252
5 4FC7 COA 2.03252
6 4FC7 NAP 2.03252
7 5OJI NAP 2.03252
8 5OJI ISN 2.03252
9 5FFF 5XC 2.03252
10 3C3N FMN 2.43902
11 5T2U NAP 2.43902
12 4C3Y ANB 2.84553
13 1NZY BCA 2.84553
14 2GN3 MAN 2.84553
15 3TY3 GGG 2.84553
16 1Q19 APC 2.84553
17 2GN3 MMA 2.84553
18 3NUG NAD 2.84553
19 1UKZ ADP 2.95567
20 3NC9 TR3 3.25203
21 2PD4 NAD 3.25203
22 4GKV NAD 3.25203
23 2PD4 DCN 3.25203
24 2BD0 NAP 3.27869
25 5FEU NAP 3.65854
26 3GJX GTP 3.65854
27 4KOT CE3 3.7037
28 4RF2 NAP 4.06504
29 3GMB FAD 4.06504
30 4EIP FAD 4.06504
31 4EIP K2C 4.06504
32 3PA8 621 4.06504
33 1XG5 NAP 4.06504
34 3A28 NAD 4.26357
35 5BRT FAD 4.47154
36 5VN0 FAD 4.47154
37 5VN0 NAI 4.47154
38 1EU1 MGD 4.47154
39 3MJY FMN 4.47154
40 3MJY IJZ 4.47154
41 5X68 FAD 4.87805
42 3SJU NDP 4.87805
43 2NU5 NAG 4.91803
44 2HYR BGC GLC 4.91803
45 2GUC MAN 4.91803
46 2GUD MAN 4.91803
47 2HYQ MAN MAN 4.91803
48 2NUO BGC 4.91803
49 3TN7 NJP 5.05837
50 3RJ5 NAD 5.51181
51 1PN0 FAD 5.69106
52 1PN0 IPH 5.69106
53 4RQU NAD 5.69106
54 1X1R GDP 5.69106
55 2Y6Q FAD 5.69106
56 6CA4 MLI 6.09756
57 1UM0 FMN 6.09756
58 1Z83 AP5 6.12245
59 3IHZ FK5 6.34921
60 1GEG NAD 6.64062
61 5EVY FAD 6.91057
62 1ON3 MCA 6.91057
63 4J36 1HR 6.91057
64 4J36 FAD 6.91057
65 5YGE ACO 6.91057
66 3E1T FAD 7.22656
67 1YKJ PHB 7.31707
68 1YKJ FAD 7.31707
69 2JAH NDP 7.69231
70 1EBF NAD 7.72358
71 4CNK FAD 7.72358
72 4K5S FAD 8.13008
73 2RGX AP5 8.73786
74 4CQM NAP 9.42623
75 1QF9 ALF 9.79381
76 1QF9 ADP 9.79381
77 1QF9 C5P 9.79381
78 2CFC NAD 10.1626
79 2JAP NDP 10.1626
80 6FHO FAD 10.5691
81 3TWO NDP 12.6016
82 2WYV NAD 14.6341
83 2NP9 YE1 14.6341
84 2F5Z FAD 15.4472
85 3D3W NAP 15.4472
86 1XPM CAA 23.1707
87 3AI8 HNQ 43.0894
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