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Receptor
PDB id Resolution Class Description Source Keywords
5LY2 2.43 Å EC: 1.14.11.- JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND MACROCYCLIC PEP INHIBITOR CP2_R6KME3 (13-MER) HOMO SAPIENS JMJD2A KDM4A OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATDIOXYGENASE OXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FTRIAD DEMETHYLASE HISTONE JMJC DOMAIN METAL BINDING PROEPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: HIGHLY SELECTIVE INHIBITION OF HISTONE DEMETHYLASES NOVO MACROCYCLIC PEPTIDES. NAT COMMUN V. 8 14773 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI C:501;
D:402;
A:501;
B:402;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
58.693 Ni [Ni+2...
CL D:404;
D:401;
B:404;
C:503;
B:401;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
GOL B:408;
B:407;
A:504;
A:505;
B:406;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
OGA B:405;
C:504;
A:503;
D:405;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
ZN D:403;
A:502;
B:403;
C:502;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LY2 2.43 Å EC: 1.14.11.- JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND MACROCYCLIC PEP INHIBITOR CP2_R6KME3 (13-MER) HOMO SAPIENS JMJD2A KDM4A OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATDIOXYGENASE OXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FTRIAD DEMETHYLASE HISTONE JMJC DOMAIN METAL BINDING PROEPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: HIGHLY SELECTIVE INHIBITION OF HISTONE DEMETHYLASES NOVO MACROCYCLIC PEPTIDES. NAT COMMUN V. 8 14773 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 5LY2 - OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 5LY2 - OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5LY2 - OGA C4 H5 N O5 C(C(=O)O)N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: OGA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 OGA 1 1
2 AAC 0.461538 0.827586
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LY2; Ligand: OGA; Similar sites found with APoc: 149
This union binding pocket(no: 1) in the query (biounit: 5ly2.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1DRY AKG 1.23457
2 1DRY AAG 1.23457
3 4JKV 1KS 1.31234
4 2WBP ZZU 1.67598
5 2WBP SIN 1.67598
6 4OJ8 AKG 1.70648
7 4OJ8 2TQ 1.70648
8 5FPX GLY SER SER HIS HIS HIS HIS HIS 1.76991
9 1ODM ASV 1.81269
10 1NX4 AKG 1.8315
11 3ZDS HQ9 1.83727
12 3ZDS HMQ 1.83727
13 3ZDS OMD 1.83727
14 3ZDS M8O 1.83727
15 1QW9 KHP 1.83727
16 5KOD AMP 1.83727
17 5JWP AKG 1.98864
18 1H2K OGA 2.00573
19 1H2M OGA 2.00573
20 3P3N AKG 2.00573
21 4B7E OGA 2.00573
22 2WA4 069 2.00573
23 4YRD 3IT 2.22841
24 3QP6 HL6 2.26415
25 2X06 NAD 2.32558
26 3WW2 LPK 2.34375
27 4QNW FMN 2.3622
28 5O9W AKG 2.45232
29 4NAO AKG 2.45399
30 3TYZ PAB 2.5
31 3TYZ XHP 2.5
32 5YBN AKG 2.54777
33 3W21 AKG 2.5641
34 6EOZ 58K 2.5974
35 6EOZ AKG 2.5974
36 3KV5 OGA 2.62467
37 3KV4 OGA 2.62467
38 3PUA OGA 2.62467
39 4BG1 IVL 2.62467
40 4BG1 OGA 2.62467
41 2PYW ADP 2.62467
42 4B0T ADP 2.62467
43 6BQ6 TER 2.71903
44 4H3Q ANP 2.76243
45 1C3V NDP 2.85714
46 4HSJ 6PC 2.87356
47 2Q1W NAD 2.88714
48 1OIK AKG 2.99003
49 1OIJ AKG 2.99003
50 4R5Z SIN 2.99728
51 4UX9 ANP 3.02198
52 5WZN A2G 3.14961
53 5EPA AKG 3.22581
54 2FB3 GTP 3.23529
55 1G63 FMN 3.31492
56 2FHK MFN 3.37838
57 5LUN ARG 3.40909
58 5LUN OGA 3.40909
59 4QM9 CYS 3.46821
60 2RDQ AKG 3.47222
61 5C5T AKG 3.50877
62 4FE2 AIR 3.52941
63 1J3R 6PG 3.67454
64 5C3R HMU 3.79009
65 5C3R AKG 3.79009
66 1UNB AKG 3.85852
67 1UNB PN1 3.85852
68 4J25 OGA 3.93013
69 4WUJ FMN 4.08163
70 3H7J PPY 4.11523
71 5HV0 AKG 4.14747
72 5SVV FMN 4.37956
73 5VSM MET 4.40252
74 5VSM 5AD 4.40252
75 5YW0 SIN 4.40252
76 4QXB OGA 4.41176
77 4M26 ZZU 4.46194
78 4M26 SIN 4.46194
79 2JIG PD2 4.46429
80 5Y72 DST 4.47761
81 5HCY 60D 4.53172
82 4C5N ACP 4.71014
83 4C5N PXL 4.71014
84 5JNN 6LM 4.73684
85 4ZXA H8N 4.7619
86 2ET1 GLV 4.97512
87 2YG2 S1P 5.23256
88 4IAW LIZ 5.31915
89 2FCU AKG 5.43131
90 5G4J EXT 5.51181
91 1DZK PRZ 5.73248
92 5UQD AKG 5.77428
93 1AUX AGS 5.78778
94 6F4T OGA 5.88235
95 1GP6 SIN 5.89888
96 1GP6 QUE 5.89888
97 1GP6 DH2 5.89888
98 3E2M E2M 5.94595
99 1RZM PEP 6.21302
100 5NIU 8YZ 6.25
101 5IQT AKG 6.34921
102 1NNU TCT 6.66667
103 1NNU NAD 6.66667
104 4K38 SAM 6.75676
105 4R57 ACO 6.81818
106 4XCB HY0 6.89655
107 5L9V OGA 7.14286
108 5L9B AKG 7.14286
109 5X7Q GLC GLC GLC BGC 7.87402
110 4D9C PMP 7.89474
111 2C49 ADN 7.94702
112 5I0U DCY 8
113 5TFZ 7BC 8
114 4Y3O OGA 8.13648
115 4CCO OGA 8.13648
116 4JZR 4JR 8.33333
117 3ACL 3F1 8.44595
118 2GC0 PAN 8.51064
119 2BYC FMN 8.75912
120 1GZW GAL BGC 8.95522
121 5XEG AKG 9.09091
122 1OS7 TAU 9.54064
123 1OS7 AKG 9.54064
124 6ES0 BW8 9.77918
125 3LU1 UD2 9.89011
126 4XAC AKG 9.92064
127 4RPO T6C 10.3139
128 6FXR AKG 10.4987
129 2V0U FMN 10.9589
130 4CCN OGA 11.2861
131 4CCK OGA 11.5486
132 1LRH NLA 13.4969
133 1WBI BTN 13.9535
134 4LA7 A1O 14.2857
135 3WSJ MK1 14.6552
136 3PUR 2HG 16.5354
137 3N9O OGA 16.5354
138 3N9Q OGA 16.5354
139 3N9P OGA 16.5354
140 3E85 BSU 18.9873
141 5NCJ SIN 21.4286
142 1X0P FAD 26.5734
143 2Y0I AKG 28.5714
144 2XUM OGA 30
145 5MBC FMN 35.7143
146 4IGQ OGA 41.3889
147 4IGQ THR M3L GLN 41.3889
148 1W0O DAN 42.8571
149 5IVE 6E8 47.8788
Pocket No.: 2; Query (leader) PDB : 5LY2; Ligand: OGA; Similar sites found with APoc: 25
This union binding pocket(no: 2) in the query (biounit: 5ly2.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2XIQ MLC 1.83727
2 5XVG 8FX 2.04778
3 4A01 2PN 2.3622
4 5V1B 8UY 2.91667
5 1OIK C26 2.99003
6 3QP8 HL0 3.26087
7 3STK PLM 3.78788
8 1MI3 NAD 4.03727
9 4M26 AKG 4.46194
10 3JRS A8S 4.80769
11 3EW2 BTN 5.18518
12 4U98 ACP 5.24934
13 3KDJ A8S 5.37975
14 3WG6 NDP 5.53746
15 3DLS ADP 5.67164
16 4Q0P 0MK 5.76923
17 3B8X G4M 6.03675
18 4L80 1VU 6.32184
19 4MLO PAM 6.52174
20 4K37 SAM 6.75676
21 4XCB AKG 6.89655
22 5I8T LAC 7.26257
23 6DAM PQQ 7.87402
24 5EZU MYR 16.8539
25 6FKW PQQ 28.5714
Pocket No.: 3; Query (leader) PDB : 5LY2; Ligand: OGA; Similar sites found with APoc: 20
This union binding pocket(no: 3) in the query (biounit: 5ly2.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 5LRT ADP 1.83727
2 1YKD CMP 1.83727
3 5AE2 FYC 2.09974
4 3HX3 RET 2.8481
5 3CKJ CIT 3.03951
6 1PK8 ATP 4.72441
7 3MPB FRU 4.87805
8 1Y0G 8PP 5.2356
9 4Y30 49L 5.41311
10 5IQT 6CU 6.34921
11 5TS5 FAD 7.34908
12 1KGI T4A 7.87402
13 4BJ8 BTN 7.93651
14 4Z28 BTN 8.95522
15 2Z77 HE7 12.2302
16 6HDT BTN 12.782
17 1DY4 SNP 21.4286
18 5NCJ HL5 21.4286
19 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 29.5918
20 2RFZ CTR 42.8571
Pocket No.: 4; Query (leader) PDB : 5LY2; Ligand: OGA; Similar sites found with APoc: 10
This union binding pocket(no: 4) in the query (biounit: 5ly2.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 4PIO AVI 1.85759
2 4PIO SAH 1.85759
3 4CYI ATP 2.62467
4 5ZCT ANP 3.26797
5 1QXO FMN 3.86598
6 5H2U 1N1 4.49438
7 4P42 PEE 4.72441
8 5B2E MQG 6.25
9 5FBN 5WF 6.27306
10 1QD1 FON 12
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