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 (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4CCO - OGA C4 H5 N O5 C(C(=O)O)N....
2 4Y3O - OGA C4 H5 N O5 C(C(=O)O)N....
3 4CCN - 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: 111
This union binding pocket(no: 1) in the query (biounit: 4y3o.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2QZT PLM 0.02226 0.41327 None
2 4TW7 37K 0.03449 0.40174 None
3 4YLL 4E3 0.01916 0.41266 1.38504
4 3OPT AKG 0.0001352 0.47956 1.60858
5 2ZYI STE 0.0124 0.42471 1.71674
6 5VZ0 ADP 0.002738 0.445 1.93133
7 5LUN ARG 0.0007969 0.49074 1.98864
8 5LUN OGA 0.0002678 0.48548 1.98864
9 4B2G V1N 0.02365 0.40514 2.14592
10 1GP6 QUE 0.006054 0.44116 2.24719
11 1GP6 SIN 0.00568 0.44116 2.24719
12 1GP6 DH2 0.00568 0.44116 2.24719
13 5A3T MMK 0.00002382 0.57948 2.36052
14 5I0U DCY 0.005771 0.42093 2.5
15 5TCI 79V 0.0255 0.4052 2.53623
16 3ZDS OMD 0.01595 0.40255 2.54042
17 3ZDS HMQ 0.01721 0.4025 2.54042
18 3AVS OGA 0.000008612 0.56507 2.7897
19 3AVR OGA 0.000008185 0.53654 2.7897
20 4UF0 MMK 0.0008619 0.46814 2.7897
21 1OIJ AKG 0.00009133 0.4803 2.99003
22 5FWJ MMK 0.00002967 0.53645 3.00429
23 4QJP V1F 0.02968 0.40368 3.04183
24 5L9B AKG 0.003472 0.40328 3.1746
25 5EPA AKG 0.0006288 0.46834 3.22581
26 3HQR OGA 0.007784 0.41505 3.25203
27 5V1B 8UY 0.01209 0.40444 3.33333
28 5UQD AKG 0.002136 0.42835 3.39367
29 4RFR RHN 0.000001315 0.63122 3.44828
30 1GQG DCD 0.003759 0.45001 3.71429
31 5L4S 6KX 0.04951 0.40764 3.77358
32 5L4S NAP 0.04951 0.40764 3.77358
33 5C3R AKG 0.0009063 0.40094 3.79009
34 5C3R HMU 0.0009063 0.40094 3.79009
35 4XCB AKG 0.002811 0.43277 3.83142
36 4XCB HY0 0.01505 0.41927 3.83142
37 1OS7 AKG 0.00001428 0.42755 3.88693
38 1OS7 TAU 0.00001428 0.42755 3.88693
39 2IXC TRH 0.01078 0.42725 3.9604
40 5HV0 AKG 0.00002176 0.55106 4.14747
41 3F7Z 34O 0.01673 0.40599 4.28571
42 4M26 ZZU 0.0008898 0.48461 4.3956
43 4M26 SIN 0.0008898 0.48461 4.3956
44 4M26 AKG 0.0006029 0.46182 4.3956
45 4NBU NAI 0.02629 0.41718 4.4
46 4YRD 3IT 0.004978 0.41074 4.45682
47 5TFZ 7BC 0.001525 0.45304 4.66667
48 2OG7 SIN 0.0001897 0.46643 4.7619
49 4J25 OGA 0.00002443 0.51476 4.80349
50 3H9A PPY 0.0009075 0.45828 4.93827
51 1ODM ASV 0.005587 0.4427 5.13595
52 5KR7 6X9 0.0002315 0.49458 5.17711
53 3EW2 BTN 0.005467 0.42838 5.18518
54 5IVE 6E8 0.0001935 0.52951 5.45455
55 4ER2 IVA VAL VAL STA ALA STA 0.02912 0.4193 5.45455
56 5L9V OGA 0.00279 0.40064 5.55556
57 2WCJ M21 0.02357 0.40766 5.67376
58 5C5T AKG 0.000246 0.44892 5.70175
59 1J3R 6PG 0.003479 0.4371 5.78947
60 5JNN 6LM 0.038 0.40093 5.78947
61 4IGQ THR M3L GLN 0.00002362 0.56053 5.83333
62 4IGQ OGA 0.0000005569 0.56053 5.83333
63 2IUW AKG 0.006402 0.44597 5.88235
64 4XAC AKG 0.0005817 0.46498 5.95238
65 4GGZ BTN 0.008766 0.41837 6.08696
66 3H7J PPY 0.0002974 0.42116 6.17284
67 1L2T ATP 0.01995 0.40918 6.38298
68 2FCU AKG 0.0007089 0.46339 6.38978
69 5AA4 6X4 0.01207 0.43464 6.43016
70 4P7X AKG 0.0002913 0.49641 6.50685
71 4P7X YCP 0.0002913 0.49641 6.50685
72 5FP3 3JI 0.00002569 0.56541 6.65236
73 1QY1 PRZ 0.02632 0.40515 6.89655
74 2YG2 S1P 0.01804 0.40825 6.97674
75 2ARC ARA 0.001463 0.45406 7.31707
76 3VHH VHH 0.03053 0.431 7.31707
77 3AMN CBI 0.02931 0.40677 7.54717
78 3AMN CBK 0.02931 0.40677 7.54717
79 4NPL AKG 0.0001212 0.498 7.6
80 2FTB OLA 0.04836 0.4017 8
81 5LY2 OGA 0.0001295 0.49259 8.13648
82 5FWE OGA 0.0002201 0.47965 8.13648
83 2OS2 OGA 0.0002971 0.47733 8.13648
84 2YBP 2HG 0.0003274 0.47551 8.13648
85 5HQ0 LZ9 0.02525 0.40174 8.33333
86 5F3I 5UJ 0.000331 0.54052 8.61111
87 2Q8C AKG 0.0001671 0.48644 8.80682
88 2Q8E OGA 0.0002597 0.48041 8.80682
89 2P5B OGA 0.0005673 0.47513 8.80682
90 4LIT AKG 0.0003362 0.51199 9.58231
91 5M0T AKG 0.003875 0.42236 9.86395
92 5TO8 7FM 0.04449 0.40596 9.92908
93 4ZU4 4TG 0.02391 0.40022 10.1351
94 4QXB OGA 0.003706 0.42974 10.2941
95 4OCT AKG 0.0002777 0.43825 10.3604
96 4UAC ACR 0.02418 0.40488 10.5
97 2JIG PD2 0.00001835 0.54629 10.7143
98 5UIU 8CG 0.007112 0.44531 11.4551
99 1DMY AZM 0.008102 0.41546 11.6935
100 4BJ8 BTN 0.01325 0.41385 11.9048
101 1DRY AKG 0.000715 0.49142 14.1975
102 1DRY AAG 0.000715 0.49142 14.1975
103 4GJY OGA 0.0000004573 0.61966 16.1702
104 2XUM OGA 0.00002268 0.53195 16.3324
105 4QM9 CYS 0.009991 0.40025 16.763
106 2RDQ AKG 0.0003061 0.50618 17.0139
107 5FLJ QUE 0.01585 0.41313 19.3548
108 4Q0L V14 0.01335 0.42214 36.3636
109 1TKB N1T 0.04623 0.40714 45.4545
110 2R5N R5P 0.04515 0.40614 45.4545
111 2R5N TPP 0.04515 0.40614 45.4545
Pocket No.: 2; Query (leader) PDB : 4Y3O; 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: 4y3o.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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