Receptor
PDB id Resolution Class Description Source Keywords
5KK4 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE PLANT DEFENSIN NSD7 BOUND TO PHOSPH ACID NICOTIANA SUAVEOLENS X NICOTIANA TABACORGANISM_TAXID: 157071 DEFENSIN PHOSPHOLIPID OLIGOMER PHOSPHATIDIC ACID ANTIMICPROTEIN
Ref.: BINDING OF PHOSPHATIDIC ACID BY NSD7 MEDIATES THE F OF HELICAL DEFENSIN-LIPID OLIGOMERIC ASSEMBLIES AND PERMEABILIZATION. PROC.NATL.ACAD.SCI.USA V. 113 11202 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
44E D:103;
D:102;
C:101;
F:101;
E:102;
F:102;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
368.36 C15 H29 O8 P CCCCC...
EDO F:104;
B:102;
F:106;
D:101;
C:106;
C:105;
F:103;
A:101;
D:104;
D:105;
D:107;
D:106;
B:103;
F:105;
E:101;
C:103;
A:102;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
SO4 C:102;
A:103;
E:103;
B:105;
B:101;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
ACT C:104;
A:104;
B:104;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KK4 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE PLANT DEFENSIN NSD7 BOUND TO PHOSPH ACID NICOTIANA SUAVEOLENS X NICOTIANA TABACORGANISM_TAXID: 157071 DEFENSIN PHOSPHOLIPID OLIGOMER PHOSPHATIDIC ACID ANTIMICPROTEIN
Ref.: BINDING OF PHOSPHATIDIC ACID BY NSD7 MEDIATES THE F OF HELICAL DEFENSIN-LIPID OLIGOMERIC ASSEMBLIES AND PERMEABILIZATION. PROC.NATL.ACAD.SCI.USA V. 113 11202 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5KK4 - 44E C15 H29 O8 P CCCCCC(=O)....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4CQK - PIO C25 H49 O19 P3 CCCCCCCC(=....
2 5KK4 - 44E C15 H29 O8 P CCCCCC(=O)....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4CQK - PIO C25 H49 O19 P3 CCCCCCCC(=....
2 5KK4 - 44E C15 H29 O8 P CCCCCC(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 44E; Similar ligands found: 82
No: Ligand ECFP6 Tc MDL keys Tc
1 44E 1 1
2 PD7 0.88 1
3 LPP 0.846154 1
4 3PH 0.846154 1
5 7PH 0.846154 1
6 6PH 0.846154 1
7 7P9 0.830189 1
8 M7U 0.721311 1
9 44G 0.683333 0.911111
10 PX2 0.672414 0.930233
11 PSF 0.66129 0.803922
12 CD4 0.609375 0.953488
13 TGL 0.603774 0.690476
14 PEF 0.6 0.788462
15 PEV 0.6 0.788462
16 PTY 0.6 0.788462
17 PEH 0.6 0.788462
18 8PE 0.6 0.788462
19 XP5 0.590909 0.727273
20 LHG 0.590909 0.911111
21 PEE 0.590909 0.773585
22 9PE 0.590909 0.788462
23 PGT 0.590909 0.911111
24 CDL 0.575758 0.863636
25 PC7 0.573529 0.727273
26 6PL 0.573529 0.727273
27 HGP 0.573529 0.727273
28 HGX 0.573529 0.727273
29 PLD 0.573529 0.727273
30 P5S 0.573529 0.803922
31 LIO 0.573529 0.727273
32 PIF 0.56338 0.857143
33 PII 0.557143 0.836735
34 CN3 0.541667 0.953488
35 PIO 0.540541 0.857143
36 52N 0.540541 0.857143
37 IP9 0.540541 0.875
38 3PE 0.536232 0.711538
39 PIZ 0.533333 0.875
40 AGA 0.528571 0.869565
41 L9Q 0.527027 0.773585
42 LOP 0.527027 0.773585
43 MC3 0.521127 0.685185
44 PC1 0.521127 0.685185
45 PCF 0.521127 0.685185
46 PGW 0.52 0.891304
47 CN6 0.513889 0.953488
48 DR9 0.513158 0.891304
49 PGV 0.513158 0.891304
50 DGA 0.508475 0.697674
51 DDR 0.508475 0.697674
52 L2C 0.508475 0.697674
53 P6L 0.506494 0.891304
54 PGK 0.506494 0.854167
55 PCW 0.506494 0.714286
56 OZ2 0.5 0.891304
57 B7N 0.493671 0.82
58 PCK 0.493671 0.689655
59 ZPE 0.493506 0.773585
60 NKN 0.491803 0.953488
61 DGG 0.4875 0.854167
62 GP7 0.47561 0.773585
63 3PC 0.472222 0.666667
64 PEK 0.469136 0.773585
65 P3A 0.469136 0.851064
66 PIE 0.469136 0.764706
67 PSC 0.464286 0.714286
68 L9R 0.4625 0.672727
69 PC5 0.457143 0.603448
70 LBR 0.454545 0.644444
71 T7X 0.436782 0.82
72 DB4 0.43662 0.795918
73 DLP 0.435294 0.672727
74 PBU 0.432432 0.795918
75 PDK 0.428571 0.683333
76 NKP 0.428571 0.931818
77 EPH 0.422222 0.773585
78 SQD 0.414634 0.609375
79 PIB 0.413333 0.795918
80 5P5 0.413333 0.795918
81 2JT 0.403509 0.659091
82 G2A 0.403509 0.659091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KK4; Ligand: 44E; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5kk4.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5KK4; Ligand: 44E; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5kk4.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5KK4; Ligand: 44E; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5kk4.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5KK4; Ligand: 44E; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5kk4.bio1) has 2 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5KK4; Ligand: 44E; Similar sites found: 17
This union binding pocket(no: 5) in the query (biounit: 5kk4.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4ZGS NAD 0.01376 0.42678 None
2 3F5O UOC COA 0.02714 0.41365 None
3 4ER2 IVA VAL VAL STA ALA STA 0.04313 0.41209 None
4 4U60 SIA 0.006367 0.41173 None
5 3EMY IVA VAL VAL STA ALA STA 0.02188 0.40666 None
6 4U60 SIA GAL NGA 0.008404 0.40553 None
7 3GNE FLC 0.02437 0.40542 None
8 4CNG SAH 0.03569 0.40284 None
9 1Z4O GL1 0.03825 0.40149 None
10 1J49 NAD 0.04243 0.40131 None
11 4X7G 3Y8 0.006234 0.45431 4.16667
12 5B4B LP5 0.04536 0.40509 8.33333
13 4YC0 5OF 0.03425 0.40123 10.4167
14 4RQU NAD 0.03996 0.40066 10.4167
15 3ATY FMN 0.02452 0.40805 12.5
16 1J39 UPG 0.03736 0.40533 14.5833
17 1D1T NAD 0.03377 0.40842 16.6667
Pocket No.: 6; Query (leader) PDB : 5KK4; Ligand: 44E; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5kk4.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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