Receptor
PDB id Resolution Class Description Source Keywords
3KV4 2.19 Å EC: 2.-.-.- STRUCTURE OF PHF8 IN COMPLEX WITH HISTONE H3 HOMO SAPIENS EPIGENETICS HISTONE CODE COVALENT HISTONE MODIFICATIONS JUMONJI DEMETHYLASE MENTAL RETARDATION METAL-BINDING ZINC ZINC-FINGER
Ref.: ENZYMATIC AND STRUCTURAL INSIGHTS FOR SUBSTRATE SPECIFICITY OF A FAMILY OF JUMONJI HISTONE LYSINE DEMETHYLASES. NAT.STRUCT.MOL.BIOL. V. 17 38 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:452;
A:453;
A:454;
A:455;
A:456;
A:457;
A:458;
A:459;
A:460;
A:461;
A:462;
A:463;
A:464;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
FE2 A:450;
Part of Protein;
none;
submit data
55.845 Fe [Fe+2...
NI A:451;
Invalid;
none;
submit data
58.693 Ni [Ni+2...
OGA A:5798;
Valid;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
ZN A:448;
A:449;
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
3KV4 2.19 Å EC: 2.-.-.- STRUCTURE OF PHF8 IN COMPLEX WITH HISTONE H3 HOMO SAPIENS EPIGENETICS HISTONE CODE COVALENT HISTONE MODIFICATIONS JUMONJI DEMETHYLASE MENTAL RETARDATION METAL-BINDING ZINC ZINC-FINGER
Ref.: ENZYMATIC AND STRUCTURAL INSIGHTS FOR SUBSTRATE SPECIFICITY OF A FAMILY OF JUMONJI HISTONE LYSINE DEMETHYLASES. NAT.STRUCT.MOL.BIOL. V. 17 38 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 3KV4 - 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 211 families.
1 3KV4 - 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 166 families.
1 3KV4 - 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 : 3KV4; Ligand: OGA; Similar sites found: 119
This union binding pocket(no: 1) in the query (biounit: 3kv4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZJ3 G6P 0.02823 0.4006 1.6
2 1AUX AGS 0.02043 0.40585 1.92926
3 2XMY CDK 0.03785 0.4288 2.01342
4 4BG1 IVL 0.02229 0.40876 2.06718
5 2IUW AKG 0.001488 0.45098 2.10084
6 4IGQ THR M3L GLN 0.01768 0.40865 2.22222
7 4IGQ OGA 0.001604 0.40496 2.22222
8 5A3T MMK 0.004422 0.45494 2.23714
9 5FWJ MMK 0.002414 0.41946 2.23714
10 4XCB HY0 0.002645 0.46359 2.29885
11 4XCB AKG 0.001499 0.44771 2.29885
12 5JSP DQY 0.006179 0.40361 2.48756
13 2FCU AKG 0.00256 0.43291 2.55591
14 1GQG DCD 0.02703 0.40309 2.57143
15 5LY2 OGA 0.0002147 0.48316 2.62467
16 5FWE OGA 0.0003075 0.4755 2.62467
17 2OS2 OGA 0.0004448 0.46921 2.62467
18 2YBP 2HG 0.0007333 0.45865 2.62467
19 5KR7 6X9 0.0001041 0.45938 2.7248
20 3KFC 61X 0.04774 0.40358 2.7668
21 5F3I 5UJ 0.005399 0.47188 2.77778
22 2P5B OGA 0.0006972 0.47193 2.84091
23 2Q8E OGA 0.000439 0.46956 2.84091
24 3OPT AKG 0.0001621 0.4913 2.94906
25 1MOQ GLP 0.01855 0.40891 2.98913
26 5C5T AKG 0.001707 0.42189 3.07018
27 4UF0 MMK 0.003611 0.43779 3.13199
28 1NX4 AKG 0.0005288 0.467 3.2967
29 1SO2 666 0.01225 0.41463 3.33333
30 3AVS OGA 0.0001305 0.50284 3.3557
31 4KQI RBZ 0.03458 0.40993 3.37079
32 2VEG PMM 0.01201 0.40667 3.50318
33 4R38 RBF 0.01949 0.40874 3.57143
34 5EPA AKG 0.00004706 0.52066 3.58423
35 4YRD 3IT 0.001279 0.44539 3.62117
36 5UIU 8CG 0.02302 0.41868 3.71517
37 3R96 AMP 0.02743 0.42156 3.7234
38 3R96 ACO 0.02743 0.42156 3.7234
39 5M0T AKG 0.003805 0.42457 3.7415
40 4EKV BTN 0.008519 0.41709 3.77358
41 3PQB VGP 0.01252 0.42205 3.79242
42 3KPB SAM 0.008751 0.42581 4.09836
43 4NPL AKG 0.01174 0.40078 4.4
44 2A1L PCW 0.02405 0.42953 4.44444
45 1IS3 LAT 0.004269 0.4001 4.44444
46 3MPB FRU 0.0004791 0.4855 4.47154
47 4AMV F6R 0.0181 0.4054 4.47427
48 5I0U DCY 0.00004453 0.52846 4.5
49 1ODM ASV 0.0005926 0.49642 4.53172
50 4M69 ANP 0.01901 0.41016 4.79233
51 5TZ6 7OD 0.01432 0.40663 4.87013
52 4NAO AKG 0.0001092 0.46884 4.90798
53 2GQS C2R 0.01799 0.40245 5.06329
54 3WUC GLC GAL 0.02328 0.40794 5.10949
55 3EW2 BTN 0.00179 0.4464 5.18518
56 2JIG PD2 0.005132 0.42442 5.35714
57 2A1X AKG 0.0004439 0.42871 5.51948
58 3T03 3T0 0.01565 0.4079 5.59284
59 2ZSC BTN 0.01129 0.41391 5.67376
60 5LUN OGA 0.002151 0.42855 5.68182
61 1DRY AAG 0.001436 0.47888 5.8642
62 1GP6 QUE 0.01942 0.41809 5.89888
63 1GP6 SIN 0.01828 0.41809 5.89888
64 1OS7 TAU 0.008043 0.42983 6.00707
65 5V1B 8UY 0.0009163 0.44507 6.25
66 4TW7 37K 0.02619 0.40976 6.25
67 1OIJ AKG 0.001061 0.42625 6.31229
68 1OIK C26 0.02165 0.40163 6.31229
69 1OIK AKG 0.007412 0.40055 6.31229
70 4LS7 1X9 0.01874 0.40498 6.33803
71 3E2M E2M 0.03769 0.40113 6.48649
72 4P7X AKG 0.003591 0.44404 6.50685
73 1VYF OLA 0.02765 0.4072 6.66667
74 1UNB PN1 0.004204 0.45725 6.75241
75 1UNB AKG 0.003739 0.45725 6.75241
76 3W21 AKG 0.0002473 0.45373 6.95971
77 4M26 ZZU 0.002463 0.46495 7.14286
78 4M26 SIN 0.002463 0.46495 7.14286
79 4M26 AKG 0.007685 0.40904 7.14286
80 1LRH NLA 0.00009631 0.5133 7.36196
81 4XAC AKG 0.00001349 0.5451 7.53968
82 2Y0I AKG 0.00002932 0.52684 8.52273
83 1H2M OGA 0.0000117 0.54501 8.59599
84 2XUM OGA 0.000008388 0.53468 8.59599
85 4B7E OGA 0.00002085 0.53426 8.59599
86 1H2K OGA 0.00001322 0.52538 8.59599
87 3P3N AKG 0.00001491 0.52297 8.59599
88 2WA4 069 0.00005736 0.46789 8.59599
89 4J25 OGA 0.001266 0.44872 9.17031
90 1FM9 570 0.02023 0.42065 9.19118
91 1OI6 TMP 0.01523 0.40352 9.26829
92 2CM4 RCL 0.01991 0.41014 9.33333
93 4OCT AKG 0.001141 0.46001 9.90991
94 1K7L 544 0.02499 0.4113 10.7639
95 4BNU 9KQ 0.01332 0.42096 10.7807
96 4RFR RHN 0.006703 0.43127 10.8374
97 4GJY OGA 0.00004264 0.50235 11.4894
98 4BJ8 BTN 0.01866 0.40397 11.9048
99 5FLJ QUE 0.006907 0.43462 12.3656
100 4QM9 CYS 0.0007043 0.44859 12.7168
101 4JZR 4JR 0.001172 0.4568 14.8148
102 2C4I BTN 0.0167 0.40662 15.1292
103 5HV0 AKG 0.000823 0.47319 15.2074
104 5DJT FMN 0.003158 0.44896 16.3934
105 4WN5 MVC 0.02992 0.40243 16.5217
106 4BQY FNT 0.0002198 0.40384 17.0635
107 5L9B AKG 0.0004535 0.43886 17.4603
108 3HQR OGA 0.0005347 0.47961 17.4797
109 3G08 FEE 0.04977 0.41816 18.1818
110 3RUG DB6 0.04318 0.41543 18.1818
111 2RDQ AKG 0.001988 0.46218 18.75
112 3D72 FAD 0.04602 0.40046 18.7919
113 5A5W GUO 0.04468 0.41033 20.8333
114 5UQD AKG 0.0002661 0.48571 25
115 2GC0 PAN 0.01015 0.42051 26.5957
116 5I8T LAC 0.01213 0.4022 28.4916
117 5L9V OGA 0.0004351 0.43768 31.5789
118 3AVR OGA 0.00005923 0.5128 36.3636
119 3PUR 2HG 0.000000006085 0.71122 48.3221
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