Receptor
PDB id Resolution Class Description Source Keywords
2Z5U 2.25 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 HOMO SAPIENS CHROMATIN HISTONE DEMETHYLASE NUCLEOSOME TRANSCRIPTION LLYSINE-SPECIFIC CHROMATIN REGULATOR FAD NUCLEUS OXIDOREPHOSPHORYLATION REPRESSOR TRANSCRIPTION REGULATION STRUCGENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL ANFUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: CRYSTAL STRUCTURE OF HISTONE DEMETHYLASE LSD1 AND TRANYLCYPROMINE AT 2.25 A BIOCHEM.BIOPHYS.RES.COMMUN. V. 366 15 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAJ A:1;
Valid;
none;
submit data
919.725 C36 H43 N9 O16 P2 Cc1cc...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6KGQ 2.32 Å EC: 1.-.-.- LSD1-FCPA-MPE FIVE-MEMBERED RING ADDUCT MODEL HOMO SAPIENS DEMETHYLASE AMINE OXIDASE CHROMATIN HISTONE FAD MECHANIINHIBITOR OXIDOREDUCTASE
Ref.: DEVELOPMENT AND STRUCTURAL EVALUATION OF N-ALKYLATE TRANS-2-PHENYLCYCLOPROPYLAMINE-BASED LSD1 INHIBITOR CHEMMEDCHEM V. 15 787 2020
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 383 families.
1 6KGP - DJ0 FAD n/a n/a
2 6KGO Ki = 0.37 uM DJ0 FAD n/a n/a
3 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
4 2Z5U - FAJ C36 H43 N9 O16 P2 Cc1cc2c(cc....
5 2DW4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 6KGQ Ki = 9 nM DJC FAD n/a n/a
7 6KGR - DJC FAD n/a n/a
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 337 families.
1 6KGP - DJ0 FAD n/a n/a
2 6KGO Ki = 0.37 uM DJ0 FAD n/a n/a
3 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
4 2Z5U - FAJ C36 H43 N9 O16 P2 Cc1cc2c(cc....
5 2DW4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 6KGQ Ki = 9 nM DJC FAD n/a n/a
7 6KGR - DJC FAD n/a n/a
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 225 families.
1 6KGP - DJ0 FAD n/a n/a
2 6KGO Ki = 0.37 uM DJ0 FAD n/a n/a
3 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
4 2Z5U - FAJ C36 H43 N9 O16 P2 Cc1cc2c(cc....
5 2DW4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 6KGQ Ki = 9 nM DJC FAD n/a n/a
7 6KGR - DJC FAD n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: FAJ; Similar ligands found: 80
No: Ligand ECFP6 Tc MDL keys Tc
1 FAJ 1 1
2 FA9 0.606936 0.963855
3 SFD 0.603659 0.842105
4 FDA 0.575758 0.886364
5 FAS 0.57485 0.97561
6 FAD 0.57485 0.97561
7 F2N 0.573864 0.88764
8 6FA 0.562874 0.963855
9 FNK 0.552326 0.877778
10 62F 0.543353 0.916667
11 FAY 0.531429 0.963415
12 RFL 0.528409 0.941176
13 JNT 0.527778 0.855422
14 UBG 0.505618 0.963855
15 P6G FDA 0.505435 0.909091
16 DJ0 FAD 0.487562 0.88764
17 6YU 0.472637 0.861702
18 CNV FAD 0.464865 0.88764
19 FAD NBT 0.462366 0.821053
20 DAL FAD PER 0.455497 0.819149
21 FAD T2C 0.450777 0.821053
22 FAD CNX 0.445026 0.814433
23 A2D 0.442857 0.853659
24 FAD NBA 0.441624 0.795918
25 P5F 0.439791 0.91954
26 FYA 0.43871 0.865854
27 APR 0.431507 0.831325
28 AR6 0.431507 0.831325
29 T5A 0.431138 0.873563
30 AP0 0.430303 0.816092
31 DLL 0.428571 0.843373
32 M33 0.427586 0.843373
33 FAE 0.427027 0.963855
34 BA3 0.426573 0.853659
35 DQV 0.425926 0.865854
36 FB0 0.425414 0.836957
37 TXE 0.424242 0.869048
38 B4P 0.423611 0.853659
39 AP5 0.423611 0.853659
40 A3R 0.422078 0.869048
41 B5M 0.421384 0.857143
42 FA5 0.421384 0.86747
43 48N 0.420732 0.880952
44 3OD 0.420382 0.855422
45 AGS 0.418919 0.793103
46 AD9 0.418919 0.811765
47 NAX 0.418182 0.83908
48 OAD 0.416667 0.855422
49 DJC FAD 0.415888 0.829787
50 ACP 0.414966 0.833333
51 ATP 0.414966 0.831325
52 HEJ 0.414966 0.831325
53 139 0.414201 0.860465
54 ADP 0.413793 0.831325
55 P33 FDA 0.413265 0.819149
56 A1R 0.412903 0.869048
57 5FA 0.412162 0.831325
58 AQP 0.412162 0.831325
59 HQG 0.411765 0.821429
60 BIS 0.411392 0.784091
61 AN2 0.410959 0.821429
62 AT4 0.410959 0.802326
63 6V0 0.409639 0.837209
64 A22 0.409091 0.843373
65 GTA 0.408537 0.872093
66 ATF 0.407895 0.802326
67 9X8 0.407643 0.813953
68 OOB 0.406452 0.843373
69 8LH 0.405229 0.823529
70 ANP 0.403974 0.811765
71 ACQ 0.403974 0.833333
72 PAJ 0.403846 0.848837
73 4AD 0.403846 0.857143
74 PRX 0.402685 0.811765
75 5AL 0.401316 0.843373
76 4UW 0.401198 0.806818
77 TXD 0.401198 0.869048
78 DND 0.401198 0.845238
79 8LQ 0.4 0.845238
80 QA7 0.4 0.835294
Similar Ligands (3D)
Ligand no: 1; Ligand: FAJ; 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 : 6KGQ; Ligand: DJC FAD; Similar sites found with APoc: 48
This union binding pocket(no: 1) in the query (biounit: 6kgq.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
1 3QJ4 FAD 2.33918
2 1V59 NAD 4.60251
3 7C3H FAD 5.74074
4 7C3H FAD 5.74074
5 7C3H LYS 5.74074
6 7C3H LYS 5.74074
7 3K7M FAD 6.11765
8 5YB7 ORN 6.37931
9 5YB7 FAD 6.37931
10 5YB7 ORN 6.37931
11 5YB7 FAD 6.37931
12 5YB7 FAD 6.37931
13 5YB7 ORN 6.37931
14 5YB7 ORN 6.37931
15 5YB7 FAD 6.37931
16 2VVL FAD 6.46465
17 2VVL FAD 6.46465
18 2VVL FAD 6.46465
19 2VVL FAD 6.46465
20 2VVL FAD 6.46465
21 2VVL FAD 6.46465
22 2VVL FAD 6.46465
23 2VVM FAD 6.46465
24 2VVL FAD 6.46465
25 2VVM FAD 6.46465
26 2JB2 PHE 7.15746
27 2JB2 FAD 7.15746
28 2JB2 PHE 7.15746
29 2JB2 FAD 7.15746
30 4IV9 FAD 7.89946
31 4IV9 FAD 7.89946
32 1REO FAD 8.05785
33 2YG3 FAD 14.128
34 2YG3 FAD 14.128
35 1RSG FAD 21.124
36 1RSG FAD 21.124
37 1YY5 FAD 22.807
38 1YY5 FAD 22.807
39 5MBX FAD 23.34
40 5MBX SP5 23.34
41 5TS5 FAD 24.7934
42 5TS5 FAD 24.7934
43 1H82 GZZ 29.8701
44 1H82 GZZ 29.8701
45 1H82 FAD 29.8701
46 1H82 FAD 29.8701
47 1H82 GZZ 29.8701
48 1H82 FAD 29.8701
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