Receptor
PDB id Resolution Class Description Source Keywords
2Z3Y 2.25 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF LYSINE-SPECIFIC DEMETHYLASE1 HOMO SAPIENS CHROMATIN CRYSTAL STRUCTURE HISTONE DEMETHYLASE NUCLEOSOME TRANSCRIPTION LSD1 LYSINE-SPECIFIC ALTERNATIVE SPLICING CHROMATIN REGULATOR COILED COIL FADNUCLEUS OXIDOREDUCTASE PHOSPHORYLATION REPRESSOR TRANSCRIPTION REGULATION STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: CRYSTAL STRUCTURE OF HISTONE DEMETHYLASE LSD1 AND TRANYLCYPROMINE AT 2.25A BIOCHEM.BIOPHYS.RES.COMMUN. V. 366 15 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
F2N A:1;
Valid;
none;
submit data
919.725 C36 H43 N9 O16 P2 Cc1cc...
View in 3D viewer
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: F2N; Similar ligands found: 111
No: Ligand ECFP6 Tc MDL keys Tc
1 F2N 1 1
2 FNK 0.833333 0.965909
3 DJC FAD 0.675978 0.934066
4 CNV FAD 0.654321 0.932584
5 FDA 0.647436 0.976744
6 6YU 0.646067 0.924731
7 SFD 0.595092 0.772277
8 FAD NBT 0.591716 0.882979
9 DAL FAD PER 0.58046 0.902174
10 FAJ 0.573864 0.88764
11 FAD T2C 0.573864 0.903226
12 FAD CNX 0.568965 0.894737
13 FAS 0.566265 0.886364
14 FAD 0.566265 0.886364
15 6FA 0.554217 0.876405
16 FA9 0.553672 0.91954
17 FAD NBA 0.552486 0.894737
18 RFL 0.537572 0.857143
19 62F 0.534884 0.875
20 FAY 0.531792 0.875
21 JNT 0.528169 0.816092
22 UBG 0.497175 0.897727
23 9OC 0.496644 0.895349
24 P5F 0.494505 0.9
25 FB0 0.491228 0.840426
26 P6G FDA 0.48913 0.849462
27 APR 0.460993 0.793103
28 AR6 0.460993 0.793103
29 DJ0 FAD 0.458128 0.849462
30 9OU 0.456954 0.883721
31 48N 0.455696 0.8
32 A2D 0.452555 0.813953
33 B5M 0.448052 0.818182
34 3OD 0.447368 0.816092
35 FYA 0.447368 0.825581
36 DLL 0.446667 0.804598
37 OAD 0.443709 0.816092
38 DQV 0.443038 0.825581
39 OOB 0.442953 0.804598
40 FA5 0.43871 0.827586
41 M33 0.43662 0.804598
42 8LQ 0.436242 0.806818
43 BA3 0.435714 0.813953
44 GTA 0.433962 0.813187
45 AP5 0.432624 0.813953
46 B4P 0.432624 0.813953
47 ANP 0.431507 0.795455
48 PAJ 0.430464 0.791209
49 AP0 0.429448 0.840909
50 P1H 0.429379 0.865169
51 AGS 0.427586 0.777778
52 QA7 0.426667 0.797753
53 6V0 0.425926 0.862069
54 9X8 0.424837 0.777778
55 ATP 0.423611 0.813953
56 HEJ 0.423611 0.813953
57 TXE 0.423313 0.872093
58 OMR 0.423313 0.784946
59 EAD 0.422857 0.863636
60 ADP 0.422535 0.813953
61 T5A 0.421687 0.897727
62 AQP 0.42069 0.813953
63 5FA 0.42069 0.813953
64 B5Y 0.420382 0.818182
65 P33 FDA 0.419689 0.842105
66 AT4 0.41958 0.786517
67 AN2 0.41958 0.804598
68 PTJ 0.419355 0.8
69 5AL 0.418919 0.804598
70 8LE 0.418919 0.797753
71 FAE 0.418478 0.876405
72 AD9 0.417808 0.795455
73 DND 0.417178 0.806818
74 NAI 0.417178 0.850575
75 CA0 0.416667 0.795455
76 ATF 0.416107 0.786517
77 3UK 0.415584 0.816092
78 8QN 0.414474 0.804598
79 COD 0.414201 0.827957
80 9SN 0.414013 0.78022
81 KG4 0.413793 0.795455
82 ACP 0.413793 0.816092
83 8LH 0.413333 0.786517
84 B5V 0.412903 0.806818
85 A1R 0.411765 0.829545
86 A3R 0.411765 0.829545
87 CNA 0.410714 0.827586
88 HQG 0.410596 0.804598
89 1ZZ 0.410256 0.774194
90 00A 0.409091 0.769231
91 AHX 0.409091 0.8
92 TXD 0.408537 0.850575
93 NAX 0.408537 0.885057
94 A22 0.407895 0.825581
95 50T 0.40411 0.784091
96 6YZ 0.403974 0.816092
97 SRP 0.403974 0.806818
98 G3A 0.403727 0.820225
99 ACQ 0.402685 0.816092
100 AMO 0.402597 0.827586
101 ADQ 0.402597 0.795455
102 4AD 0.402597 0.818182
103 45A 0.401408 0.772727
104 ABM 0.401408 0.772727
105 PRX 0.401361 0.795455
106 TXA 0.401274 0.806818
107 G5P 0.401235 0.820225
108 AFH 0.401235 0.771739
109 80F 0.401163 0.835165
110 AMP 0.4 0.790698
111 A 0.4 0.790698
Similar Ligands (3D)
Ligand no: 1; Ligand: F2N; 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
APoc FAQ
Feedback