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Receptor
PDB id Resolution Class Description Source Keywords
5FWE 2.05 Å EC: 1.14.11.- JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15) R3ME2S PEPTIDE HOMO SAPIENS JMJD2A OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATE DIOXOXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FACIAL TRIAD DEMETHYLASE HISTONE JMJC DOMAIN METAL BINDING PROTEIN EPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: ARGININE DEMETHYLATION IS CATALYSED BY A SUBSET OF HISTONE LYSINE DEMETHYLASES. NAT.COMMUN. V. 7 11974 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI B:1356;
A:1355;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
CL A:1357;
B:1358;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
GOL B:1360;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
OGA A:1358;
B:1359;
Valid;
Valid;
none;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
ZN A:1356;
B:1357;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FWE 2.05 Å EC: 1.14.11.- JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15) R3ME2S PEPTIDE HOMO SAPIENS JMJD2A OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATE DIOXOXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FACIAL TRIAD DEMETHYLASE HISTONE JMJC DOMAIN METAL BINDING PROTEIN EPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: ARGININE DEMETHYLATION IS CATALYSED BY A SUBSET OF HISTONE LYSINE DEMETHYLASES. NAT.COMMUN. V. 7 11974 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 5FWE - 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 5FWE - 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 5FWE - 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 : 5FWE; Ligand: OGA; Similar sites found with APoc: 155
This union binding pocket(no: 1) in the query (biounit: 5fwe.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 4JKV 1KS 1.31234
2 5DXI TRE 1.65563
3 2WBP ZZU 1.67598
4 2WBP SIN 1.67598
5 4OJ8 AKG 1.70648
6 4OJ8 2TQ 1.70648
7 5FPX GLY SER SER HIS HIS HIS HIS HIS 1.76991
8 1ODM ASV 1.81269
9 1NX4 AKG 1.8315
10 3ZDS HMQ 1.83727
11 3ZDS HQ9 1.83727
12 3ZDS OMD 1.83727
13 3ZDS M8O 1.83727
14 1QW9 KHP 1.83727
15 5KOD AMP 1.83727
16 5JWP AKG 1.98864
17 1H2K OGA 2.00573
18 1H2M OGA 2.00573
19 4B7E OGA 2.00573
20 3P3N AKG 2.00573
21 2WA4 069 2.00573
22 4YRD 3IT 2.22841
23 3QP6 HL6 2.26415
24 2X06 NAD 2.32558
25 3WW2 LPK 2.34375
26 3WW2 SF6 2.34375
27 5O9W AKG 2.45232
28 4NAO AKG 2.45399
29 3TYZ PAB 2.5
30 3TYZ XHP 2.5
31 5YBN AKG 2.54777
32 4N14 WR7 2.54777
33 3W21 AKG 2.5641
34 6EOZ 58K 2.5974
35 6EOZ AKG 2.5974
36 2HFN FMN 2.61438
37 3KV5 OGA 2.62467
38 3KV4 OGA 2.62467
39 3PUA OGA 2.62467
40 4BG1 OGA 2.62467
41 4BG1 IVL 2.62467
42 2PYW ADP 2.62467
43 4H3Q ANP 2.76243
44 1C3V NDP 2.85714
45 4HSJ 6PC 2.87356
46 5Z46 8XL 2.91262
47 1OIK AKG 2.99003
48 1OIK C26 2.99003
49 1OIJ AKG 2.99003
50 4R5Z SIN 2.99728
51 4UX9 ANP 3.02198
52 5EPA AKG 3.22581
53 5HES 032 3.25733
54 3QP8 HL0 3.26087
55 5ZCT ANP 3.26797
56 1G63 FMN 3.31492
57 5LUN OGA 3.40909
58 5LUN ARG 3.40909
59 4QM9 CYS 3.46821
60 2RDQ AKG 3.47222
61 5C5T AKG 3.50877
62 1J3R 6PG 3.67454
63 5C3R AKG 3.79009
64 5C3R HMU 3.79009
65 1UNB PN1 3.85852
66 1UNB AKG 3.85852
67 4J25 OGA 3.93013
68 4WUJ FMN 4.08163
69 3H7J PPY 4.11523
70 5HV0 AKG 4.14747
71 5MBC FMN 4.24929
72 5YW0 SIN 4.40252
73 5VSM MET 4.40252
74 4QXB OGA 4.41176
75 4M26 ZZU 4.46194
76 4M26 SIN 4.46194
77 4M26 AKG 4.46194
78 2JIG PD2 4.46429
79 5HCY 60D 4.53172
80 3BXO UPP 4.60251
81 4LA7 A1O 4.66321
82 4C5N ACP 4.71014
83 4C5N PXL 4.71014
84 4ZXA H8N 4.7619
85 4NJH 2K8 4.78261
86 4NJH SAM 4.78261
87 3JRS A8S 4.80769
88 3EW2 BTN 5.18518
89 2YG2 S1P 5.23256
90 4U98 ACP 5.24934
91 4IAW LIZ 5.31915
92 3GC8 B45 5.40541
93 2FCU AKG 5.43131
94 3WG6 NDP 5.53746
95 5NCJ SIN 5.59701
96 3DLS ADP 5.67164
97 3L2B B4P 5.71429
98 1DZK PRZ 5.73248
99 4Q0P 0MK 5.76923
100 5UQD AKG 5.77428
101 1AUX AGS 5.78778
102 6F4T OGA 5.88235
103 3E2M E2M 5.94595
104 1RZM PEP 6.21302
105 4MLO PAM 6.52174
106 1YRX FMN 6.61157
107 4K38 SAM 6.75676
108 4K2M O1G 6.77201
109 2PR5 FMN 6.81818
110 4R57 ACO 6.81818
111 4XCB HY0 6.89655
112 4XCB AKG 6.89655
113 5L9V OGA 7.14286
114 5L9B AKG 7.14286
115 5I8T LAC 7.26257
116 1W0O DAN 7.34908
117 5TBM 79A 7.82609
118 6DAM PQQ 7.87402
119 2C49 ADN 7.94702
120 5I0U DCY 8
121 5TFZ 7BC 8
122 5FS0 5JC 8.05687
123 4CCO OGA 8.13648
124 4Y3O OGA 8.13648
125 4JZR 4JR 8.33333
126 3ACL 3F1 8.44595
127 2GC0 PAN 8.51064
128 1GZW GAL BGC 8.95522
129 1OS7 AKG 9.54064
130 1OS7 TAU 9.54064
131 4XAC AKG 9.92064
132 4CCN OGA 11.2861
133 4CCK OGA 11.5486
134 1QD1 FON 12
135 1LRH NLA 13.4969
136 1WBI BTN 13.9535
137 3WSJ MK1 14.6552
138 3N0Y APC 15.6425
139 3PUR 2HG 16.5354
140 3N9O OGA 16.5354
141 3N9Q OGA 16.5354
142 3N9P OGA 16.5354
143 1X0P FAD 26.5734
144 2Y0I AKG 28.5714
145 2XUM OGA 30
146 5XEG AKG 33.3333
147 3E85 BSU 33.3333
148 5WZN A2G 33.3333
149 5IQT AKG 33.3333
150 1J0D 5PA 33.3333
151 6FXR AKG 40
152 4IGQ OGA 41.3889
153 4IGQ THR M3L GLN 41.3889
154 5G4J EXT 46.6667
155 5IVE 6E8 47.8788
Pocket No.: 2; Query (leader) PDB : 5FWE; Ligand: OGA; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 5fwe.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1DRY AKG 1.23457
2 1DRY AAG 1.23457
3 5HWO HMG 1.83727
4 1FWY UD1 2.1148
5 2A1X AKG 2.27273
6 2PP3 LGT 2.88714
7 5VSM 5AD 4.40252
8 4IJP 1EH 4.46927
9 5Y72 DST 4.47761
10 5JNN 6LM 4.73684
11 3KDJ A8S 5.37975
12 1GP6 QUE 5.89888
13 1GP6 DH2 5.89888
14 1GP6 SIN 5.89888
15 3B8X G4M 6.03675
16 2GQS C2R 8.43882
17 2BYC FMN 8.75912
18 5EZU MYR 16.8539
19 5HZX 2GE 33.3333
20 5IQT 6CU 33.3333
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