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...
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90% Homology Family
Leader
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
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 352 families.
1 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
2 2Z5U - FAJ n/a n/a
3 2DW4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
2 2Z5U - FAJ n/a n/a
3 2DW4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 207 families.
1 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
2 2Z5U - FAJ n/a n/a
3 2DW4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: F2N; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 F2N 1 1
2 FNK 0.833333 0.965909
3 FDA 0.647436 0.976744
4 6YU 0.646067 0.924731
5 SFD 0.595092 0.772277
6 FAD NBT 0.591716 0.882979
7 FAD CNX 0.568965 0.894737
8 FAS 0.566265 0.886364
9 FAD 0.566265 0.886364
10 6FA 0.554217 0.876405
11 FA9 0.553672 0.91954
12 FAD NBA 0.552486 0.894737
13 RFL 0.537572 0.857143
14 62F 0.534884 0.875
15 FAY 0.531792 0.875
16 9OC 0.496644 0.895349
17 P5F 0.494505 0.9
18 FB0 0.491228 0.840426
19 P6G FDA 0.48913 0.849462
20 APR 0.460993 0.793103
21 AR6 0.460993 0.793103
22 9OU 0.456954 0.883721
23 48N 0.455696 0.8
24 A2D 0.452555 0.813953
25 B5M 0.448052 0.818182
26 3OD 0.447368 0.816092
27 FYA 0.447368 0.825581
28 DLL 0.446667 0.804598
29 OAD 0.443709 0.816092
30 DQV 0.443038 0.825581
31 OOB 0.442953 0.804598
32 FA5 0.43871 0.827586
33 M33 0.43662 0.804598
34 8LQ 0.436242 0.806818
35 BA3 0.435714 0.813953
36 GTA 0.433962 0.813187
37 B4P 0.432624 0.813953
38 AP5 0.432624 0.813953
39 ANP 0.431507 0.795455
40 PAJ 0.430464 0.791209
41 AP0 0.429448 0.840909
42 P1H 0.429379 0.865169
43 SAP 0.427586 0.777778
44 AGS 0.427586 0.777778
45 6V0 0.425926 0.862069
46 9X8 0.424837 0.777778
47 ATP 0.423611 0.813953
48 HEJ 0.423611 0.813953
49 OMR 0.423313 0.784946
50 TXE 0.423313 0.872093
51 EAD 0.422857 0.863636
52 ADP 0.422535 0.813953
53 T5A 0.421687 0.897727
54 5FA 0.42069 0.813953
55 AQP 0.42069 0.813953
56 B5Y 0.420382 0.818182
57 P33 FDA 0.419689 0.842105
58 AN2 0.41958 0.804598
59 AT4 0.41958 0.786517
60 PTJ 0.419355 0.8
61 5AL 0.418919 0.804598
62 8LE 0.418919 0.797753
63 FAE 0.418478 0.876405
64 AD9 0.417808 0.795455
65 DND 0.417178 0.806818
66 NAI 0.417178 0.850575
67 NXX 0.417178 0.806818
68 CA0 0.416667 0.795455
69 ATF 0.416107 0.786517
70 3UK 0.415584 0.816092
71 8QN 0.414474 0.804598
72 COD 0.414201 0.827957
73 9SN 0.414013 0.78022
74 ACP 0.413793 0.816092
75 KG4 0.413793 0.795455
76 8LH 0.413333 0.786517
77 B5V 0.412903 0.806818
78 A3R 0.411765 0.829545
79 A1R 0.411765 0.829545
80 CNA 0.410714 0.827586
81 HQG 0.410596 0.804598
82 1ZZ 0.410256 0.774194
83 AHX 0.409091 0.8
84 00A 0.409091 0.769231
85 NAX 0.408537 0.885057
86 TXD 0.408537 0.850575
87 A22 0.407895 0.825581
88 50T 0.40411 0.784091
89 SRP 0.403974 0.806818
90 6YZ 0.403974 0.816092
91 G3A 0.403727 0.820225
92 ACQ 0.402685 0.816092
93 ADQ 0.402597 0.795455
94 4AD 0.402597 0.818182
95 AMO 0.402597 0.827586
96 YAP 0.402516 0.818182
97 ABM 0.401408 0.772727
98 45A 0.401408 0.772727
99 PRX 0.401361 0.795455
100 TXA 0.401274 0.806818
101 AFH 0.401235 0.771739
102 G5P 0.401235 0.820225
103 80F 0.401163 0.835165
104 A 0.4 0.790698
105 AMP 0.4 0.790698
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Z3Y; Ligand: F2N; Similar sites found with APoc: 46
This union binding pocket(no: 1) in the query (biounit: 2z3y.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
1 3QJ4 FAD 2.33918
2 3QJ4 FAD 2.33918
3 1V59 NAD 4.60251
4 5ZBC FAD 5.54324
5 5ZBC FAD 5.54324
6 3X0V FAD 5.73013
7 3X0V FAD 5.73013
8 2VVL FAD 6.46465
9 2VVL FAD 6.46465
10 2VVL FAD 6.46465
11 2VVL FAD 6.46465
12 2VVL FAD 6.46465
13 2VVL FAD 6.46465
14 2VVL FAD 6.46465
15 2VVM FAD 6.46465
16 2VVL FAD 6.46465
17 2VVM FAD 6.46465
18 2IVD FAD 6.69456
19 2IVD FAD 6.69456
20 2JB2 FAD 7.15746
21 2JB2 FAD 7.15746
22 2JB2 PHE 7.15746
23 2JB2 PHE 7.15746
24 5G3U FDA 7.32861
25 5G3U FDA 7.32861
26 2YG3 FAD 7.72627
27 2YG3 FAD 7.72627
28 4IV9 FAD 7.89946
29 4IV9 FAD 7.89946
30 1REO FAD 8.02469
31 4ZCC FAD 13.9881
32 4ZCC FAD 13.9881
33 1RSG FAD 21.124
34 1RSG FAD 21.124
35 1YY5 FAD 22.807
36 1YY5 FAD 22.807
37 5MBX FAD 23.34
38 5MBX SP5 23.34
39 5TS5 FAD 24.7934
40 5TS5 FAD 24.7934
41 5TS5 FAD 24.7934
42 5TS5 FAD 24.7934
43 1H82 FAD 29.2373
44 1H82 FAD 29.2373
45 1H82 FAD 29.2373
46 1H82 GZZ 29.2373
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