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Receptor
PDB id Resolution Class Description Source Keywords
4Y3O 2.2 Å EC: 1.14.11.-1.14.11.27 CRYSTAL STRUCTURE OF RIBOSOMAL OXYGENASE NO66 IN COMPLEX WIT SUBSTRATE RPL8 PEPTIDE AND NI(II) AND COFACTOR N-OXALYGLYCI HOMO SAPIENS RIBOSOMAL OXYGENASE QUATERNARY COMPOUND STRUCTURE JMJC-DOMOXIDOREDUCTASE-PEPTIDE COMPLEX
Ref.: STRUCTURE OF THE JMJC DOMAIN-CONTAINING PROTEIN NO6 COMPLEXED WITH RIBOSOMAL PROTEIN RPL8. ACTA CRYSTALLOGR.,SECT.D V. 71 1955 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT B:706;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
GOL B:703;
B:705;
B:704;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NI A:701;
B:701;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
OGA A:702;
B:702;
Valid;
Valid;
none;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4Y3O 2.2 Å EC: 1.14.11.-1.14.11.27 CRYSTAL STRUCTURE OF RIBOSOMAL OXYGENASE NO66 IN COMPLEX WIT SUBSTRATE RPL8 PEPTIDE AND NI(II) AND COFACTOR N-OXALYGLYCI HOMO SAPIENS RIBOSOMAL OXYGENASE QUATERNARY COMPOUND STRUCTURE JMJC-DOMOXIDOREDUCTASE-PEPTIDE COMPLEX
Ref.: STRUCTURE OF THE JMJC DOMAIN-CONTAINING PROTEIN NO6 COMPLEXED WITH RIBOSOMAL PROTEIN RPL8. ACTA CRYSTALLOGR.,SECT.D V. 71 1955 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4Y3O - 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 1 families.
1 4Y3O - 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 1 families.
1 4Y3O - 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 : 4Y3O; Ligand: OGA; Similar sites found with APoc: 192
This union binding pocket(no: 1) in the query (biounit: 4y3o.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2QZT PLM None
2 4TW7 37K None
3 1UNB PN1 1.60772
4 1UNB AKG 1.60772
5 3OPT AKG 1.60858
6 2ZYI STE 1.71674
7 3CH6 311 1.74825
8 3CH6 NAP 1.74825
9 5VZ0 ADP 1.93133
10 1LLF F23 1.93133
11 2IHK CSF 1.93133
12 6EOZ AKG 1.94805
13 6EOZ 58K 1.94805
14 3WW2 SF6 1.95312
15 3WW2 LPK 1.95312
16 5LUN ARG 1.98864
17 5LUN OGA 1.98864
18 6ALW BMJ 2.08333
19 4B2G V1N 2.14592
20 1GP6 QUE 2.24719
21 5T8O 76Z 2.29226
22 5A3T MMK 2.36052
23 4IE6 UN9 2.36052
24 5TCI 79V 2.53623
25 3ZDS HMQ 2.54042
26 3ZDS OMD 2.54042
27 5O9W AKG 2.7248
28 3AVR OGA 2.7897
29 6FUL E7Z 2.7897
30 4UF0 MMK 2.7897
31 1OIJ AKG 2.99003
32 1OIK C26 2.99003
33 1OIK AKG 2.99003
34 5FWJ MMK 3.00429
35 5E2N V14 3.04183
36 5OX6 A1Z 3.1746
37 5L9B AKG 3.1746
38 2FLI DX5 3.18182
39 5EPA AKG 3.22581
40 3HQR OGA 3.25203
41 5V1B 8UY 3.33333
42 5UQD AKG 3.39367
43 4OJ8 AKG 3.41297
44 4OJ8 2TQ 3.41297
45 4RFR RHN 3.44828
46 6F5W KG1 3.52304
47 5FPX GLY SER SER HIS HIS HIS HIS HIS 3.53982
48 5YJS SAL 3.58974
49 2GMH UQ5 3.64807
50 1NX4 AKG 3.663
51 1GQG DCD 3.71429
52 4Z28 BTN 3.73134
53 5Y02 HBX 3.73832
54 5L4S NAP 3.77358
55 5L4S 6KX 3.77358
56 5C3R HMU 3.79009
57 5C3R AKG 3.79009
58 4XCB HY0 3.83142
59 4XCB AKG 3.83142
60 2RHQ GAX 3.86266
61 1OS7 TAU 3.88693
62 1OS7 AKG 3.88693
63 5XEG AKG 3.8961
64 2IXC TRH 3.9604
65 3NNF AKG 4.06977
66 6BFN DL1 4.09357
67 5HV0 AKG 4.14747
68 2ZSC BTN 4.25532
69 3F7Z 34O 4.28571
70 4M26 ZZU 4.3956
71 4M26 SIN 4.3956
72 4M26 AKG 4.3956
73 4NBU NAI 4.4
74 4YRD 3IT 4.45682
75 6HDT BTN 4.51128
76 4Q0P 0MK 4.61538
77 5TFZ 7BC 4.66667
78 5YW0 SIN 4.71698
79 2OG7 SIN 4.7619
80 2C1Q BTN 4.7619
81 4J25 OGA 4.80349
82 3H9A PPY 4.93827
83 5IQT AKG 5.07937
84 5IQT 6CU 5.07937
85 5YBL AKG 5.09554
86 1ODM ASV 5.13595
87 5KR7 6X9 5.17711
88 3EW2 BTN 5.18518
89 4JNJ BTN 5.21739
90 1NWW HPN 5.36913
91 4BG1 OGA 5.42636
92 4BG1 IVL 5.42636
93 5IVE 6E8 5.45455
94 4ER2 IVA VAL VAL STA ALA STA 5.45455
95 2X34 UQ8 5.52486
96 5L9V OGA 5.55556
97 4EKV BTN 5.66038
98 2WCJ M21 5.67376
99 5C5T AKG 5.70175
100 5JNN 6LM 5.78947
101 4IGQ THR M3L GLN 5.83333
102 4IGQ OGA 5.83333
103 2GC0 PAN 5.85106
104 2IUW AKG 5.88235
105 4XAC AKG 5.95238
106 4GGZ BTN 6.08696
107 3H7J PPY 6.17284
108 6FE1 V14 6.22568
109 2GDZ NAD 6.36704
110 5YBN AKG 6.36943
111 1L2T ATP 6.38298
112 2FCU AKG 6.38978
113 5AA4 6X4 6.43016
114 5YXC CIT 6.48148
115 4P7X YCP 6.50685
116 4P7X AKG 6.50685
117 3SCH TB6 6.56566
118 1ZZ7 S0H 6.56566
119 6F6D AKG 6.65236
120 5FP3 3JI 6.65236
121 2BR6 HSL 6.74603
122 1QY1 PRZ 6.89655
123 2YG2 S1P 6.97674
124 6EXF LYS 6.98925
125 2GOO NDG 7.01754
126 3VHH VHH 7.31707
127 2ARC ARA 7.31707
128 2ET1 GLV 7.46269
129 2WBP SIN 7.5419
130 2WBP ZZU 7.5419
131 3AMN CBK 7.54717
132 3AMN CBI 7.54717
133 4NPL AKG 7.6
134 2FTB OLA 8
135 5LY2 OGA 8.13648
136 5FWE OGA 8.13648
137 2OS2 OGA 8.13648
138 2YBP 2HG 8.13648
139 6H8P OGA 8.13648
140 4ZXA H8N 8.33333
141 5HQ0 LZ9 8.33333
142 5F3I 5UJ 8.61111
143 2Q8E OGA 8.80682
144 2P5B OGA 8.80682
145 6F6J SIN 8.93855
146 6F6J CUW 8.93855
147 5NCJ SIN 8.95522
148 5NCJ HL5 8.95522
149 3FW3 ETS 9.02256
150 4WO4 JLS 9.38776
151 3QRC SCR 9.55414
152 4LIT AKG 9.58231
153 4UX9 ANP 9.61539
154 5M0T AKG 9.86395
155 5TO8 7FM 9.92908
156 4ZU4 4TG 10.1351
157 4QAC KK3 10.1382
158 4QXB OGA 10.2941
159 4OCT AKG 10.3604
160 1IY8 NAD 10.4869
161 4UAC ACR 10.5
162 2JIG PD2 10.7143
163 5UIU 8CG 11.4551
164 1DMY AZM 11.6935
165 4BJ8 BTN 11.9048
166 1DRY AAG 14.1975
167 1DRY AKG 14.1975
168 2BYC FMN 14.5985
169 6F4T OGA 14.902
170 5FP4 YC8 15.5689
171 5JWP AKG 16.1932
172 2Y0I AKG 16.1932
173 2WA4 069 16.3324
174 1H2M OGA 16.3324
175 1H2K OGA 16.3324
176 2XUM OGA 16.3324
177 3P3N AKG 16.3324
178 4B7E OGA 16.3324
179 5N0L ILE 16.3522
180 2RDQ AKG 17.0139
181 5FLJ QUE 19.3548
182 1YRX FMN 23.1405
183 2JBM SRT 27.2727
184 6FXR AKG 36.3636
185 4WW8 VD9 36.3636
186 5CJF 520 36.3636
187 5ZM4 AKG 36.3636
188 4PNI KQQ 36.3636
189 1TKB N1T 45.4545
190 2R5N R5P 45.4545
191 2R5N RP5 45.4545
192 2R5N TPP 45.4545
Pocket No.: 2; Query (leader) PDB : 4Y3O; Ligand: OGA; Similar sites found with APoc: 22
This union binding pocket(no: 2) in the query (biounit: 4y3o.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 6CMJ F6J 2.18069
2 4ITU NAI 2.23048
3 1GP6 DH2 2.24719
4 1GP6 SIN 2.24719
5 3G5N PB2 2.36052
6 3ZDS HQ9 2.54042
7 3W21 AKG 2.5641
8 4H3Q ANP 3.31492
9 2JLD AG1 3.57143
10 1Q23 FUA 4.10959
11 4H69 10Y 4.12371
12 1J3R 6PG 5.78947
13 1QVJ RP5 5.82192
14 2YAJ 4HP 6.97674
15 3PUA OGA 7.14286
16 3QXV MTX 7.14286
17 2PTR 2SA 7.14286
18 5KZD RCJ 7.84983
19 1UNQ 4IP 8
20 3KXC PLM 11.3924
21 2QF7 AGS 18.1818
22 5ZM4 9FU 36.3636
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