Receptor
PDB id Resolution Class Description Source Keywords
5LJ0 1.82 Å EC: 3.6.1.3 CRYSTAL STRUCTURE OF HUMAN ATAD2 BROMODOMAIN IN COMPLEX WITH 4R,5S)-3-((4,4-DIFLUOROCYCLOHEXYL)METHOXY)-5-METHOXYPIPERIDA MINO)-3-METHYL-5-(5-METHYLPYRIDIN-3-YL)-1,7-NAPHTHYRIDIN-2 HOMO SAPIENS INHIBITOR ATAD2 BROMODOMAIN EPIGENETICS ATPASE FAMILY AACONTAINING PROTEIN 2 TRANSCRIPTION
Ref.: A CHEMICAL PROBE FOR THE ATAD2 BROMODOMAIN. ANGEW.CHEM.INT.ED.ENGL. V. 55 11382 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:1201;
A:1203;
A:1204;
A:1202;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
6XX A:1205;
Valid;
none;
ic50 = 40 nM
527.606 C28 H35 F2 N5 O3 Cc1cc...
SO4 A:1206;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LJ0 1.82 Å EC: 3.6.1.3 CRYSTAL STRUCTURE OF HUMAN ATAD2 BROMODOMAIN IN COMPLEX WITH 4R,5S)-3-((4,4-DIFLUOROCYCLOHEXYL)METHOXY)-5-METHOXYPIPERIDA MINO)-3-METHYL-5-(5-METHYLPYRIDIN-3-YL)-1,7-NAPHTHYRIDIN-2 HOMO SAPIENS INHIBITOR ATAD2 BROMODOMAIN EPIGENETICS ATPASE FAMILY AACONTAINING PROTEIN 2 TRANSCRIPTION
Ref.: A CHEMICAL PROBE FOR THE ATAD2 BROMODOMAIN. ANGEW.CHEM.INT.ED.ENGL. V. 55 11382 2016
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 0.794 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q ic50 = 13 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 5A81 ic50 = 2.512 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
5 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
6 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
7 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
8 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
9 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
10 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
11 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
12 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
13 5A83 ic50 = 130 nM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
14 5LJ0 ic50 = 40 nM 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 0.794 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q ic50 = 13 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 5A81 ic50 = 2.512 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
5 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
6 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
7 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
8 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
9 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
10 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
11 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
12 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
13 5A83 ic50 = 130 nM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
14 5LJ0 ic50 = 40 nM 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 0.794 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q ic50 = 13 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 5A81 ic50 = 2.512 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
5 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
6 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
7 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
8 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
9 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
10 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
11 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
12 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
13 5A83 ic50 = 130 nM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
14 5LJ0 ic50 = 40 nM 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6XX; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 6XX 1 1
2 6XW 0.462121 0.712644
3 NP8 0.452174 0.808219
4 YD3 0.416667 0.709302
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LJ0; Ligand: 6XX; Similar sites found: 90
This union binding pocket(no: 1) in the query (biounit: 5lj0.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CHR 4NC 0.009037 0.43315 None
2 2VWA PTY 0.008351 0.42909 None
3 2ALG DAO 0.01643 0.42042 None
4 3TL1 JRO 0.02281 0.41052 None
5 3RET PYR 0.01303 0.40683 None
6 3RET SAL 0.01303 0.40683 None
7 2QES ADE 0.03274 0.40798 1.53846
8 1YRX FMN 0.01427 0.40146 1.65289
9 5KAX RHQ 0.003087 0.45589 3.84615
10 4V3I ASP LEU THR ARG PRO 0.01178 0.43195 3.84615
11 1F4F TP3 0.01803 0.41156 3.84615
12 1UDH URA 0.02455 0.40987 3.84615
13 5H9I XAN 0.03203 0.40498 3.84615
14 4XNV BUR 0.03797 0.40014 3.84615
15 3N7S 3N7 0.03574 0.40547 4.34783
16 3FW3 GLC 0.02894 0.41185 4.61538
17 1TV5 N8E 0.03647 0.4098 4.61538
18 5FQK 6NT 0.03302 0.4039 4.61538
19 1SR7 MOF 0.006691 0.40276 4.61538
20 2HHP FLC 0.002557 0.40169 4.61538
21 4UCC ZKW 0.007824 0.43465 5.38462
22 4RW3 TDA 0.02127 0.42988 5.38462
23 3TDC 0EU 0.02956 0.42498 5.38462
24 1I0B PEL 0.0419 0.40432 5.38462
25 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.02408 0.40123 5.71429
26 5IKR ID8 0.01484 0.40782 6.15385
27 3EZ2 ADP 0.02171 0.40742 6.15385
28 1R6N 434 0.03395 0.40278 6.15385
29 3WLV AZA 0.0178 0.41617 6.92308
30 4NTO 1PW 0.02385 0.41131 6.92308
31 2GBB CIT 0.02412 0.40508 6.92308
32 4IJ6 SEP 0.03476 0.40422 6.92308
33 2VFK AMP 0.01309 0.42099 7.69231
34 1HFE CYS 0.0188 0.42024 7.69231
35 2E40 LGC 0.03045 0.4055 7.69231
36 5MBC FMN 0.003293 0.43091 8.46154
37 4OKD GLC GLC GLC 0.01913 0.42237 8.46154
38 2WR1 NAG 0.01128 0.41053 8.46154
39 4ZGM 32M 0.002805 0.47333 9.01639
40 1PCA CIT 0.005686 0.44103 9.23077
41 5HCN DAO 0.01144 0.42623 9.23077
42 5V4R MGT 0.01922 0.41819 9.23077
43 1SNN 5RP 0.009501 0.41722 9.23077
44 5U83 ZN8 0.0164 0.41804 10.7692
45 4LZB URA 0.02288 0.40782 10.7692
46 3RLF MAL 0.02742 0.40222 11.5385
47 3TW1 AHN 0.03597 0.40085 11.5385
48 2Y69 CHD 0.02744 0.41353 13.0769
49 1VAY AZA 0.0107 0.42867 14.6154
50 5MWE TCE 0.004652 0.44662 14.8148
51 3SQP 3J8 0.0106 0.42585 15.3846
52 4R78 AMP 0.02115 0.408 15.3846
53 2Q4X HMH 0.02478 0.41268 17.6923
54 3KO0 TFP 0.02369 0.40753 17.8218
55 2AJ4 GLA 0.02446 0.40892 22.3077
56 4YGM URA 0.01737 0.4118 23.0769
57 5TPX 7H7 0.0000001745 0.68234 23.5772
58 1M2Z BOG 0.009501 0.46116 23.8095
59 3MB3 MB3 0.00001895 0.54611 25.3846
60 5H6S HDH 0.01158 0.42452 25.3846
61 5F1H 5U6 0.0000009217 0.62912 26.8293
62 4UYG 73B 0.000004141 0.60959 26.9231
63 4XUB 43D 0.00000004297 0.68549 27.3504
64 3UVD MB3 0.000002344 0.6242 27.4194
65 5I8G 69E 0.000006353 0.58665 27.6923
66 5FH7 5XL 0.00000002501 0.52663 28.2258
67 5JWM 6ON 0.00001081 0.57496 29.2308
68 5N17 8FK 0.0000216 0.57129 29.2308
69 3AQA BYH 0.000001274 0.42652 29.6875
70 5I89 69B 0.000007793 0.57391 30.5085
71 4O4Z N2O 0.02578 0.41098 30.7692
72 5DW1 5GD 0.00007695 0.54116 30.9735
73 2YDW WSH 0.0000005812 0.62054 32.3077
74 4UYF 73B 0.00002013 0.57022 32.3077
75 5I7Y 69G 0.000004011 0.58816 32.6733
76 5A7C 5D4 0.00001791 0.57458 32.7434
77 4FLP JQ1 0.000006994 0.59901 32.7731
78 5FDZ 5X0 0.0000001679 0.65625 33.6134
79 5UEX 89D 0.0000003127 0.62467 34.8624
80 4YC9 4C1 0.000000004181 0.55597 35.3846
81 5VOM 9GY 0.0000001271 0.68391 36.9231
82 4BJX 73B 0.0000004081 0.65756 36.9231
83 5WUU 7UU 0.000001446 0.63611 36.9231
84 5KHM XNH 0.00000002614 0.43446 37.7953
85 5MG2 7M8 0.0000000004263 0.79803 40
86 5N49 8LW 0.00000003882 0.71068 40
87 5MGJ 7MX 0.00001493 0.57047 40.9524
88 5N18 8HZ 0.000001954 0.62572 42.2018
89 5G4R LF1 0.00000002262 0.67842 45.7627
90 5IGL BMF 0.0000003636 0.6635 46.9231
Feedback