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 318 families.
1 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
2 2Z5U - FA9 C36 H43 N9 O16 P2 Cc1cc2c(cc....
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 280 families.
1 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
2 2Z5U - FA9 C36 H43 N9 O16 P2 Cc1cc2c(cc....
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 187 families.
1 2Z3Y - F2N C36 H43 N9 O16 P2 Cc1cc2c(cc....
2 2Z5U - FA9 C36 H43 N9 O16 P2 Cc1cc2c(cc....
3 2DW4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: F2N; Similar ligands found: 97
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 P5F 0.494505 0.9
17 FB0 0.491228 0.840426
18 P6G FDA 0.48913 0.849462
19 APR 0.460993 0.793103
20 AR6 0.460993 0.793103
21 48N 0.455696 0.8
22 A2D 0.452555 0.813953
23 B5M 0.448052 0.818182
24 3OD 0.447368 0.816092
25 FYA 0.447368 0.825581
26 DLL 0.446667 0.804598
27 OAD 0.443709 0.816092
28 DQV 0.443038 0.825581
29 OOB 0.442953 0.804598
30 FA5 0.43871 0.827586
31 M33 0.43662 0.804598
32 BA3 0.435714 0.813953
33 GTA 0.433962 0.813187
34 B4P 0.432624 0.813953
35 AP5 0.432624 0.813953
36 ANP 0.431507 0.795455
37 PAJ 0.430464 0.791209
38 AP0 0.429448 0.840909
39 P1H 0.429379 0.865169
40 AGS 0.427586 0.777778
41 SAP 0.427586 0.777778
42 6V0 0.425926 0.862069
43 9X8 0.424837 0.777778
44 ATP 0.423611 0.813953
45 HEJ 0.423611 0.813953
46 TXE 0.423313 0.872093
47 OMR 0.423313 0.784946
48 EAD 0.422857 0.863636
49 ADP 0.422535 0.813953
50 T5A 0.421687 0.897727
51 5FA 0.42069 0.813953
52 AQP 0.42069 0.813953
53 B5Y 0.420382 0.818182
54 P33 FDA 0.419689 0.842105
55 AN2 0.41958 0.804598
56 AT4 0.41958 0.786517
57 PTJ 0.419355 0.8
58 5AL 0.418919 0.804598
59 FAE 0.418478 0.876405
60 AD9 0.417808 0.795455
61 DND 0.417178 0.806818
62 NXX 0.417178 0.806818
63 NAI 0.417178 0.850575
64 CA0 0.416667 0.795455
65 ATF 0.416107 0.786517
66 3UK 0.415584 0.816092
67 8QN 0.414474 0.804598
68 COD 0.414201 0.827957
69 9SN 0.414013 0.78022
70 ACP 0.413793 0.816092
71 B5V 0.412903 0.806818
72 A1R 0.411765 0.829545
73 A3R 0.411765 0.829545
74 CNA 0.410714 0.827586
75 1ZZ 0.410256 0.774194
76 AHX 0.409091 0.8
77 00A 0.409091 0.769231
78 NAX 0.408537 0.885057
79 TXD 0.408537 0.850575
80 A22 0.407895 0.825581
81 50T 0.40411 0.784091
82 SRP 0.403974 0.806818
83 6YZ 0.403974 0.816092
84 G3A 0.403727 0.820225
85 ACQ 0.402685 0.816092
86 ADQ 0.402597 0.795455
87 AMO 0.402597 0.827586
88 4AD 0.402597 0.818182
89 YAP 0.402516 0.818182
90 ABM 0.401408 0.772727
91 PRX 0.401361 0.795455
92 TXA 0.401274 0.806818
93 G5P 0.401235 0.820225
94 AFH 0.401235 0.771739
95 80F 0.401163 0.835165
96 A 0.4 0.790698
97 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: 19
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 5ZBC FAD 5.54324
3 3X0V FAD 5.73013
4 2VVL FAD 6.46465
5 2VVM FAD 6.46465
6 2IVD FAD 6.69456
7 2JB2 FAD 7.15746
8 2JB2 PHE 7.15746
9 5G3U FDA 7.32861
10 2YG3 FAD 7.72627
11 4IV9 FAD 7.89946
12 1REO FAD 8.02469
13 1RSG FAD 21.124
14 1YY5 FAD 22.807
15 5MBX FAD 23.34
16 5MBX SP5 23.34
17 5TS5 FAD 24.7934
18 1H82 FAD 29.2373
19 1H82 GZZ 29.2373
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