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 26 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 18 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: 78
This union binding pocket(no: 1) in the query (biounit: 5ly2.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DRY AAG 0.005685 0.44404 1.23457
2 1DRY AKG 0.005685 0.44404 1.23457
3 4DE9 VTP 0.02524 0.41429 1.5748
4 1ODM ASV 0.0004602 0.50122 1.81269
5 3ZDS HMQ 0.00006276 0.52468 1.83727
6 3ZDS HQ9 0.00008228 0.5081 1.83727
7 3ZDS OMD 0.0001868 0.49654 1.83727
8 3ZDS M8O 0.0002176 0.49289 1.83727
9 5KOD AMP 0.02229 0.40112 1.83727
10 1H2M OGA 0.02834 0.40324 2.00573
11 1H2K OGA 0.03059 0.40129 2.00573
12 4YRD 3IT 0.00242 0.42429 2.22841
13 4QNW FMN 0.02742 0.40403 2.3622
14 3TYZ XHP 0.01327 0.41793 2.5
15 3TYZ PAB 0.01501 0.41793 2.5
16 3W21 AKG 0.005182 0.40655 2.5641
17 3KV5 OGA 0.00008455 0.50266 2.62467
18 3KV4 OGA 0.0002147 0.48316 2.62467
19 3PUA OGA 0.00034 0.4743 2.62467
20 2PYW ADP 0.0187 0.41151 2.62467
21 4B0T ADP 0.02893 0.40792 2.62467
22 4H3Q ANP 0.01719 0.41853 2.76243
23 1OIJ AKG 0.00383 0.40853 2.99003
24 5WZN A2G 0.0151 0.40248 3.14961
25 5EPA AKG 0.00164 0.44333 3.22581
26 2FB3 GTP 0.02946 0.41166 3.23529
27 1G63 FMN 0.0234 0.40949 3.31492
28 2FHJ MFN 0.01836 0.40732 3.37838
29 5LUN ARG 0.009834 0.43396 3.40909
30 5LUN OGA 0.005835 0.41682 3.40909
31 4QM9 CYS 0.004137 0.42133 3.46821
32 2RDQ AKG 0.0003212 0.50442 3.47222
33 5C5T AKG 0.0008958 0.42445 3.50877
34 1J3R 6PG 0.01281 0.40861 3.67454
35 4J25 OGA 0.0005557 0.4526 3.93013
36 4HIA FMN 0.04424 0.40808 3.97727
37 4WUJ FMN 0.02082 0.40826 4.08163
38 5HV0 AKG 0.00002356 0.55109 4.14747
39 5SVV FMN 0.01878 0.4128 4.37956
40 5VSM MET 0.01978 0.40963 4.40252
41 5VSM 5AD 0.02284 0.40655 4.40252
42 4QXB OGA 0.000008079 0.56171 4.41176
43 4M26 ZZU 0.01743 0.41824 4.46194
44 4M26 SIN 0.01743 0.41824 4.46194
45 2JIG PD2 0.000245 0.48931 4.46429
46 5HCY 60D 0.04565 0.4072 4.53172
47 5JNN 6LM 0.02372 0.40848 4.73684
48 4ZXA H8N 0.0003774 0.4396 4.7619
49 2YG2 S1P 0.02967 0.40191 5.23256
50 2YG2 FLC 0.03656 0.40076 5.23256
51 2FCU AKG 0.007289 0.40811 5.43131
52 5UQD AKG 0.000005926 0.56165 5.77428
53 1GP6 SIN 0.008866 0.43126 5.89888
54 1GP6 DH2 0.008866 0.43126 5.89888
55 1GP6 QUE 0.009432 0.43126 5.89888
56 4K38 SAM 0.02175 0.40546 6.75676
57 5X7Q GLC GLC GLC BGC 0.02298 0.40762 7.87402
58 4D9C PMP 0.03332 0.40188 7.89474
59 5I0U DCY 0.0001117 0.51108 8
60 5TFZ 7BC 0.001138 0.45561 8
61 4Y3O OGA 0.0001295 0.49259 8.13648
62 3ACL 3F1 0.01629 0.40503 8.44595
63 4GJY OGA 0.0000003514 0.62202 8.51064
64 4XAC AKG 0.0009495 0.45035 9.92064
65 4CCK OGA 0.0001454 0.48996 11.5486
66 1LRH NLA 0.001267 0.4568 13.4969
67 3PUR 2HG 0.00003218 0.50924 16.5354
68 3N9O OGA 0.0001708 0.48647 16.5354
69 3N9Q OGA 0.0001875 0.48478 16.5354
70 3N9P OGA 0.0002275 0.47942 16.5354
71 3E85 BSU 0.02948 0.42167 18.9873
72 1X0P FAD 0.008323 0.42094 26.5734
73 2Y0I AKG 0.03554 0.4003 28.5714
74 2XUM OGA 0.000004389 0.56638 30
75 5MBC FMN 0.009048 0.42316 35.7143
76 4IGQ THR M3L GLN 0.00000002131 0.72567 41.3889
77 4IGQ OGA 0.00000000009062 0.72567 41.3889
78 5IVE 6E8 0.00000001294 0.76294 47.8788
Pocket No.: 2; Query (leader) PDB : 5LY2; Ligand: OGA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5ly2.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5LY2; Ligand: OGA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5ly2.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5LY2; Ligand: OGA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5ly2.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback