Receptor
PDB id Resolution Class Description Source Keywords
2OS2 2.3 Å EC: 1.14.11.27 CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH HISTONE H3 PEPTID TRIMETHYLATED AT LYS36 HOMO SAPIENS FE DOUBLE-STRANDED BETA HELIX DEMETHYLASE OXYGENASE STRUGENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC OXIDOREDUCTA
Ref.: CRYSTAL STRUCTURES OF HISTONE DEMETHYLASE JMJD2A RE BASIS FOR SUBSTRATE SPECIFICITY. NATURE V. 448 87 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI A:501;
B:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
OGA A:500;
B:500;
Valid;
Valid;
none;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
ZN A:502;
B:502;
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
2OS2 2.3 Å EC: 1.14.11.27 CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH HISTONE H3 PEPTID TRIMETHYLATED AT LYS36 HOMO SAPIENS FE DOUBLE-STRANDED BETA HELIX DEMETHYLASE OXYGENASE STRUGENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC OXIDOREDUCTA
Ref.: CRYSTAL STRUCTURES OF HISTONE DEMETHYLASE JMJD2A RE BASIS FOR SUBSTRATE SPECIFICITY. NATURE V. 448 87 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 2OS2 - OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 2Q8C - AKG C5 H6 O5 C(CC(=O)O)....
2 2YBP - 2HG C5 H8 O5 C(CC(=O)O)....
3 2OS2 - OGA C4 H5 N O5 C(C(=O)O)N....
4 2Q8E - OGA C4 H5 N O5 C(C(=O)O)N....
5 2Q8D - SIN C4 H6 O4 O=C([O-])C....
6 2PXJ - OGA C4 H5 N O5 C(C(=O)O)N....
7 5A7W - 35M C19 H14 N2 O5 c1cc(ccc1C....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 2Q8C - AKG C5 H6 O5 C(CC(=O)O)....
2 2YBP - 2HG C5 H8 O5 C(CC(=O)O)....
3 2OS2 - OGA C4 H5 N O5 C(C(=O)O)N....
4 2Q8E - OGA C4 H5 N O5 C(C(=O)O)N....
5 2Q8D - SIN C4 H6 O4 O=C([O-])C....
6 2PXJ - OGA C4 H5 N O5 C(C(=O)O)N....
7 5A7W - 35M C19 H14 N2 O5 c1cc(ccc1C....
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 : 2OS2; Ligand: OGA; Similar sites found: 132
This union binding pocket(no: 1) in the query (biounit: 2os2.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DRY AAG 0.01065 0.43168 1.23457
2 1DRY AKG 0.01065 0.43168 1.23457
3 4F4P 0SB 0.03404 0.43037 1.4652
4 1VJY 460 0.006746 0.44862 1.65016
5 3ZDS HMQ 0.0002968 0.4885 1.83727
6 3ZDS HQ9 0.0004191 0.47125 1.83727
7 3ZDS OMD 0.0008028 0.46376 1.83727
8 3ZDS M8O 0.0009406 0.46024 1.83727
9 1YKD CMP 0.02382 0.40197 1.83727
10 3T1A 5MA 0.02735 0.40186 1.83727
11 1H2K OGA 0.000007429 0.55613 2.00573
12 1H2M OGA 0.000008316 0.55334 2.00573
13 3P3N AKG 0.00001275 0.54316 2.00573
14 4B7E OGA 0.00001823 0.53719 2.00573
15 2WA4 069 0.00001156 0.49857 2.00573
16 4BXF AKG 0.0009655 0.45191 2.09974
17 2I7N ACO 0.02624 0.4045 2.22222
18 4YRD 3IT 0.0008773 0.45316 2.22841
19 4QMN DB8 0.01172 0.4404 2.25806
20 2V77 PAY 0.01254 0.41381 2.26537
21 5F7V GLC GLC GLC GLC 0.01127 0.42455 2.3622
22 3B2Q ATP 0.03226 0.40357 2.3622
23 2GU8 796 0.04034 0.4229 2.37389
24 3G5D 1N1 0.02027 0.4402 2.44755
25 4YLL 4E3 0.03193 0.40129 2.49307
26 3KV5 OGA 0.0001141 0.49925 2.62467
27 3KV4 OGA 0.0004448 0.46921 2.62467
28 3PUA OGA 0.0006723 0.46122 2.62467
29 4B0T ADP 0.007681 0.43873 2.62467
30 4USF 6UI 0.009271 0.41755 2.63158
31 5BVE 4VG 0.0166 0.45003 2.77008
32 4LJ3 C2E 0.0263 0.40793 2.86738
33 3D3W NAP 0.03216 0.41347 2.86885
34 5VFC 9BA 0.04277 0.40308 2.89389
35 5DQ8 FLF 0.03083 0.40488 2.91667
36 4TWP AXI 0.03674 0.41799 2.95203
37 1OIK AKG 0.007026 0.40962 2.99003
38 5WZN A2G 0.01164 0.40613 3.14961
39 3WYJ H78 0.03629 0.43256 3.16206
40 4BKJ STI 0.008216 0.43742 3.1746
41 5EPA AKG 0.002467 0.43657 3.22581
42 5HES 032 0.008675 0.43091 3.25733
43 3QP8 HL0 0.005447 0.43336 3.26087
44 4CSV STI 0.01022 0.42945 3.27273
45 2XMY CDK 0.02578 0.44022 3.3557
46 5LUN OGA 0.005273 0.42146 3.40909
47 5LUN ARG 0.01231 0.40619 3.40909
48 4P7X AKG 0.007624 0.4274 3.42466
49 4P7X YCP 0.007624 0.4274 3.42466
50 4QM9 CYS 0.007539 0.40941 3.46821
51 5C5T AKG 0.002505 0.41621 3.50877
52 5UR1 YY9 0.0386 0.4065 3.53698
53 4P5Z Q7M 0.02201 0.42517 3.60111
54 4PAB THG 0.01673 0.40874 3.67454
55 1J3R 6PG 0.01487 0.40448 3.67454
56 2WQP WQP 0.01207 0.43012 3.72493
57 4XV1 904 0.01342 0.43388 3.76712
58 4J25 OGA 0.001413 0.44613 3.93013
59 4ASE AV9 0.02186 0.41604 3.96601
60 2OFV 242 0.006628 0.45345 3.97112
61 4HIA FMN 0.003341 0.47041 3.97727
62 5HZX 2GE 0.00316 0.43695 3.97727
63 5DKK FMN 0.01239 0.41992 4.13793
64 5HV0 AKG 0.00005898 0.52995 4.14747
65 5MF5 C2E 0.02995 0.40613 4.29688
66 5SVV FMN 0.02823 0.40237 4.37956
67 4NPL AKG 0.003543 0.42701 4.4
68 4M26 SIN 0.02574 0.41051 4.46194
69 2JIG PD2 0.0002822 0.48685 4.46429
70 4IJP 1EH 0.02658 0.40203 4.46927
71 5H2U 1N1 0.01695 0.41068 4.49438
72 4ZXA H8N 0.001099 0.43229 4.7619
73 3GZ8 APR 0.02586 0.40488 4.93827
74 4J1Q NDP 0.01893 0.42158 4.98688
75 3LVW GSH 0.02803 0.41966 4.98688
76 4N1T 2GD 0.02892 0.41405 5.03145
77 5KWY C3S 0.01241 0.41498 5.26316
78 4U0I 0LI 0.01622 0.42649 5.39683
79 2FCU AKG 0.009079 0.40686 5.43131
80 3CH6 311 0.04477 0.41983 5.59441
81 3CH6 NAP 0.04477 0.41983 5.59441
82 3AVS OGA 0.0000000002182 0.7943 5.77428
83 5FP3 3JI 0.00000004391 0.71102 5.77428
84 5UQD AKG 0.00001214 0.52907 5.77428
85 4HBM 0Y7 0.026 0.40032 5.83333
86 1GP6 DH2 0.007575 0.43785 5.89888
87 1GP6 SIN 0.007575 0.43785 5.89888
88 1GP6 QUE 0.008078 0.43785 5.89888
89 4RFR RHN 0.001066 0.47191 5.91133
90 2WEI VGG 0.01238 0.41302 6.27178
91 4UF0 MMK 0.00007646 0.52337 6.29921
92 4MLO PAM 0.01269 0.41169 6.52174
93 2HK5 1BM 0.005676 0.43914 6.66667
94 5IXJ THR 0.04034 0.40453 6.82415
95 3EWK FAD 0.02592 0.40234 7.04846
96 5L4S 6KX 0.02446 0.42325 7.2327
97 5L4S NAP 0.02446 0.42325 7.2327
98 1W0O DAN 0.007571 0.4216 7.34908
99 5IXH OTP 0.04918 0.41102 7.45342
100 4OCT AKG 0.001055 0.42549 7.65766
101 5N87 N66 0.01248 0.43696 7.66773
102 1KGI T4A 0.03012 0.40186 7.87402
103 5I0U DCY 0.000188 0.49913 8
104 5TFZ 7BC 0.001251 0.45464 8
105 4Y3O OGA 0.0002971 0.47733 8.13648
106 5MJA 7O3 0.007892 0.42355 8.85246
107 1NCQ W11 0.01403 0.4153 8.8983
108 1GZW GAL BGC 0.009142 0.43592 8.95522
109 1W6P NDG GAL 0.01616 0.41203 8.95522
110 5JKG 6LF 0.03667 0.41339 9.32476
111 3DOO SKM 0.01017 0.41298 9.38628
112 5FLJ QUE 0.01032 0.42566 9.67742
113 4XAC AKG 0.002945 0.42854 9.92064
114 2QUN FUD 0.02281 0.40103 10
115 5DEY 59T 0.01627 0.44614 10.4377
116 5XDT MB3 0.04665 0.40488 10.4987
117 2IUW AKG 0.000573 0.47102 12.605
118 1QKQ MAN 0.0003836 0.4595 12.6761
119 2RKV ZBA 0.03798 0.41242 13.1234
120 2RKV COA 0.04325 0.40592 13.1234
121 1LRH NLA 0.001904 0.44816 13.4969
122 1MDC PLM 0.02412 0.40769 26.5152
123 1X0P FAD 0.01629 0.40609 26.5734
124 2Y0I AKG 0.00002079 0.53446 28.5714
125 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.009223 0.46546 29.5918
126 2XUM OGA 0.000008741 0.5518 30
127 4LIT AKG 0.00051 0.46681 36.3636
128 5FWJ MMK 0.00000001718 0.69901 42.2572
129 5A3T MMK 0.0000000005216 0.83425 42.7822
130 4IGQ THR M3L GLN 0.000000003501 0.75957 45.4545
131 4IGQ OGA 0.00000000008885 0.69402 45.4545
132 5IVE 6E8 0.00000005616 0.72279 47.8788
Pocket No.: 2; Query (leader) PDB : 2OS2; Ligand: OGA; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 2os2.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3S7O LBV 0.004173 0.45849 1.45773
2 1GQG DCD 0.03255 0.40003 2.28571
3 2CBO TH2 0.01446 0.40168 4.34783
4 2RCU BUJ 0.01622 0.44747 4.46194
5 2HK9 SKM 0.008855 0.41179 4.72727
6 2XVD AS6 0.01042 0.4357 4.96689
7 4PVD NDP 0.01569 0.42363 9.35672
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