Receptor
PDB id Resolution Class Description Source Keywords
3OPT 2.2 Å EC: 1.14.11.27 CRYSTAL STRUCTURE OF THE RPH1 CATALYTIC CORE WITH A-KETOGLUT SACCHAROMYCES CEREVISIAE RPH1 HISTONE DEMETHYLASE CATALYTIC CORE OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF SACCHARO CEREVESIAE HISTONE DEMETHYLASE RPH1: INSIGHTS INTO SUBSTRATE SPECIFICITY AND CATALYTIC MECHANISM BIOCHEM.J. V. 433 295 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:501;
Valid;
none;
submit data
146.098 C5 H6 O5 C(CC(...
NI A:500;
Part of Protein;
none;
submit data
58.693 Ni [Ni+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3OPT 2.2 Å EC: 1.14.11.27 CRYSTAL STRUCTURE OF THE RPH1 CATALYTIC CORE WITH A-KETOGLUT SACCHAROMYCES CEREVISIAE RPH1 HISTONE DEMETHYLASE CATALYTIC CORE OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF SACCHARO CEREVESIAE HISTONE DEMETHYLASE RPH1: INSIGHTS INTO SUBSTRATE SPECIFICITY AND CATALYTIC MECHANISM BIOCHEM.J. V. 433 295 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 3OPT - AKG C5 H6 O5 C(CC(=O)O)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3OPT - AKG C5 H6 O5 C(CC(=O)O)....
50% Homology Family (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3OPT - AKG C5 H6 O5 C(CC(=O)O)....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
5 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
6 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
7 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
8 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
9 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
10 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
11 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
12 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
13 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
14 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
15 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
16 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
17 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
18 4URA ic50 = 5.01 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
19 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
20 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
21 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
22 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
23 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
24 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
25 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
26 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
27 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
28 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
29 4XDO ic50 = 11 mM OGA C4 H5 N O5 C(C(=O)O)N....
30 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
31 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
32 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
33 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
34 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
35 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
36 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
37 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
38 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKG; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 OOG 0.5 0.947368
3 69O 0.458333 0.714286
4 2IT 0.423077 0.615385
5 SHF 0.416667 0.666667
6 3PY 0.409091 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3OPT; Ligand: AKG; Similar sites found: 175
This union binding pocket(no: 1) in the query (biounit: 3opt.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4LIT AKG 0.0002585 0.48097 1.34048
2 5HCY 60D 0.001894 0.48973 1.51057
3 4Y3O OGA 0.0001352 0.47956 1.60858
4 4OCT AKG 0.003611 0.43309 1.8018
5 1DRY AKG 0.01122 0.43007 1.85185
6 1DRY AAG 0.01122 0.43007 1.85185
7 3F8D FAD 0.0438 0.43159 1.85759
8 3B8X G4M 0.0408 0.40767 1.87668
9 2WBP ZZU 0.01966 0.41195 1.95531
10 2WBP SIN 0.01966 0.41195 1.95531
11 4FE2 AIR 0.008975 0.41456 1.96078
12 2Y0I AKG 0.000004413 0.56776 1.98864
13 1H2M OGA 0.000001374 0.59369 2.00573
14 1H2K OGA 0.00000156 0.56889 2.00573
15 3P3N AKG 0.000002011 0.56369 2.00573
16 2WA4 069 0.000004281 0.51381 2.00573
17 4G31 0WH 0.01223 0.4367 2.00669
18 4P7X AKG 0.005656 0.43389 2.05479
19 4P7X YCP 0.005656 0.43389 2.05479
20 4R1S NAP 0.02992 0.40717 2.07715
21 5UQD AKG 0.0000117 0.52974 2.14477
22 1W0O DAN 0.004789 0.43132 2.14477
23 5NCY 8TK 0.04492 0.4015 2.14477
24 1NP7 FAD 0.04268 0.40107 2.14477
25 4QMN DB8 0.01912 0.42807 2.25806
26 1GQG DCD 0.01981 0.41206 2.28571
27 4JKV 1KS 0.02225 0.41272 2.41287
28 4KBA 1QM 0.005698 0.44582 2.41692
29 5W4W 9WG 0.04057 0.40379 2.41692
30 2WEI VGG 0.01696 0.40476 2.43902
31 3G5D 1N1 0.03839 0.4228 2.44755
32 1C3V NDP 0.03988 0.40639 2.44898
33 1LRH NLA 0.0003851 0.48416 2.45399
34 1OS7 TAU 0.007967 0.42842 2.4735
35 1OS7 AKG 0.007967 0.42842 2.4735
36 3TYZ XHP 0.03332 0.40142 2.5
37 3TYZ PAB 0.03747 0.40142 2.5
38 2IUW AKG 0.002158 0.44217 2.52101
39 3E85 BSU 0.01041 0.44674 2.53165
40 4EWH T77 0.01191 0.43163 2.54545
41 4HKP 16B 0.01188 0.41889 2.5641
42 1UNB PN1 0.00156 0.48009 2.57235
43 1UNB AKG 0.001377 0.48009 2.57235
44 5JKG 6LF 0.02071 0.42697 2.57235
45 3VRV YSD 0.04142 0.41853 2.58303
46 2V77 PAY 0.01616 0.40799 2.589
47 1DQX BMP 0.01175 0.42224 2.62172
48 1VJY 460 0.01233 0.43408 2.64026
49 3EWK FAD 0.02719 0.401 2.64317
50 2GU8 796 0.03472 0.42766 2.67062
51 4BXF AKG 0.0002606 0.48105 2.68097
52 4BG1 IVL 0.02036 0.41075 2.68097
53 4XCB AKG 0.0112 0.4041 2.68199
54 1ODM ASV 0.004114 0.45042 2.71903
55 2OO8 RAJ 0.02036 0.4115 2.83912
56 5VCV 1N1 0.01836 0.41691 2.89389
57 4C5N ACP 0.02529 0.41014 2.89855
58 3KV5 OGA 0.00005001 0.5178 2.94906
59 3KV4 OGA 0.0001621 0.4913 2.94906
60 1OPK P16 0.01503 0.42813 2.94906
61 4B0T ADP 0.01774 0.41865 2.94906
62 1OLM VTQ 0.02944 0.40869 2.94906
63 1O6U PLM 0.01712 0.40495 2.94906
64 5X2Z 3LM 0.03167 0.40493 2.94906
65 2I8T GDD 0.0351 0.40364 2.99401
66 4K3P ACE GLN LEU ALA LEU PHE 0.007635 0.43164 3.00546
67 2JIG PD2 0.001556 0.44947 3.125
68 5LUN OGA 0.01357 0.42584 3.125
69 5LUN ARG 0.005877 0.4222 3.125
70 5IQT AKG 0.002961 0.45138 3.1746
71 2X2M X2M 0.01204 0.42194 3.18471
72 5UR1 YY9 0.03179 0.41119 3.21543
73 3ZDS HMQ 0.0005133 0.47612 3.21716
74 3ZDS HQ9 0.0008774 0.45513 3.21716
75 3ZDS OMD 0.001758 0.4464 3.21716
76 3ZDS M8O 0.001986 0.44373 3.21716
77 5IXJ THR 0.04478 0.402 3.21716
78 3MPB FRU 0.005834 0.4286 3.25203
79 4QM9 CYS 0.003425 0.41621 3.46821
80 4U0I 0LI 0.02423 0.41765 3.49206
81 2V63 CAP 0.02987 0.40247 3.57143
82 2VDH CAP 0.03188 0.40088 3.57143
83 2V67 CAP 0.03274 0.40025 3.57143
84 1ZB6 GST 0.002281 0.47122 3.58306
85 4LOO SB4 0.002793 0.45068 3.60111
86 4YRD 3IT 0.00136 0.4092 3.62117
87 4CSV STI 0.009376 0.43159 3.63636
88 1NX4 AKG 0.009224 0.40523 3.663
89 3TAY MN0 0.01942 0.41558 3.68098
90 3E2M E2M 0.03769 0.40142 3.78378
91 5C5T AKG 0.006402 0.41855 3.94737
92 4BQY FNT 0.0108 0.42153 3.96825
93 5HZX 2GE 0.003053 0.43809 3.97727
94 4TWP AXI 0.03795 0.4176 4.05904
95 2HK5 1BM 0.01165 0.42288 4.07407
96 4XLI 1N1 0.0138 0.413 4.10448
97 4M26 SIN 0.01625 0.42149 4.12088
98 4M26 ZZU 0.01625 0.42149 4.12088
99 1X0P FAD 0.01847 0.40369 4.1958
100 4WVO 3UZ 0.01067 0.43301 4.22961
101 4NPL AKG 0.004918 0.41956 4.4
102 4BKJ STI 0.004558 0.44848 4.44444
103 1OIK AKG 0.005761 0.40445 4.65116
104 1OIK C26 0.01817 0.40445 4.65116
105 4ZXA H8N 0.004958 0.42444 4.7619
106 5DKK FMN 0.01514 0.41546 4.82759
107 5FLJ QUE 0.004186 0.44524 4.83871
108 5HV0 AKG 0.00009438 0.51882 5.06912
109 3SXF BK5 0.01056 0.44094 5.09383
110 1R6W 164 0.0154 0.40823 5.2795
111 4IAW LIZ 0.01468 0.40361 5.31915
112 2OFV 242 0.02575 0.42036 5.41516
113 2FCU AKG 0.006401 0.41234 5.43131
114 4NFN 2KC 0.02109 0.40397 5.50162
115 5MJA 7O3 0.007386 0.42534 5.57377
116 3SAO NKN 0.006775 0.42584 5.625
117 2XVD AS6 0.01177 0.43217 5.62914
118 1WDD CAP 0.03049 0.40033 5.63003
119 5JNN 6LM 0.0313 0.40362 5.78947
120 2GC0 PAN 0.01437 0.41335 5.85106
121 4RFR RHN 0.000741 0.48073 5.91133
122 2QZ3 XYP XYP XYP 0.02921 0.40043 5.94595
123 4XV1 904 0.03116 0.41463 6.16438
124 3GC8 B45 0.004449 0.44591 6.16622
125 5EFW FMN 0.02787 0.40105 6.2069
126 2GQS C2R 0.01 0.41631 6.32911
127 4XAC AKG 0.001049 0.45087 6.34921
128 4P5Z Q7M 0.02002 0.42693 6.37119
129 4RJK TPP 0.03469 0.40589 6.43432
130 5HZ9 5M8 0.028 0.40154 6.66667
131 5F7V GLC GLC GLC GLC 0.02041 0.4105 6.70241
132 5VNF VAL THR SER VAL VAL 0.01483 0.40365 6.70241
133 3SXS PP2 0.01195 0.422 6.71642
134 5EPA AKG 0.0008033 0.46053 6.81004
135 4HIA FMN 0.005449 0.45796 6.81818
136 2X06 NAD 0.03694 0.40191 6.97674
137 1J0D 5PA 0.03679 0.40178 7.03812
138 3QP8 HL0 0.01606 0.40845 7.06522
139 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.006445 0.43156 7.07965
140 4USF 6UI 0.02717 0.40824 7.23684
141 3AVS OGA 0.000000002644 0.73825 7.23861
142 3AVR OGA 0.00000006325 0.66028 7.23861
143 5H2U 1N1 0.02078 0.40622 7.49064
144 5DEY 59T 0.02355 0.43664 7.74411
145 5FP3 3JI 0.0000001045 0.69057 7.7748
146 5HES 032 0.01341 0.42098 8.14332
147 3L2B B4P 0.04408 0.40606 8.16327
148 4UF0 MMK 0.0001014 0.51689 8.31099
149 2Y6O 1N1 0.01217 0.42358 8.59107
150 3VHE 42Q 0.02025 0.41963 8.91365
151 4K3H 1OM 0.02767 0.40229 9.32203
152 2RDQ AKG 0.0009488 0.4791 9.375
153 4ASE AV9 0.03121 0.40852 9.38338
154 4MNS 2AX 0.04865 0.41413 9.43396
155 3PUA OGA 0.0009913 0.45248 9.65147
156 4K2M O1G 0.03283 0.40099 9.65147
157 1NCQ W11 0.00773 0.42814 10.2941
158 5B2E MQG 0.02239 0.40099 10.2941
159 5TFZ 7BC 0.0006207 0.47004 10.6667
160 4J25 OGA 0.005019 0.41857 10.917
161 3H7J PPY 0.00812 0.42062 10.992
162 1GT4 UNA 0.02193 0.40194 11.9497
163 4MLO PAM 0.01695 0.40517 11.9565
164 2H8H H8H 0.02102 0.40604 12.0643
165 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.02176 0.44304 13.2653
166 3RUG DB6 0.02008 0.43737 14.1414
167 1MDC PLM 0.02422 0.40752 16.6667
168 5I0U DCY 0.0001613 0.50217 18.5
169 2XUM OGA 0.000001985 0.56393 30
170 4B7E OGA 0.000004706 0.5664 35.2941
171 5A3T MMK 0.000000003233 0.79008 42.0912
172 5FWJ MMK 0.0000000456 0.67722 42.0912
173 5IVE 6E8 0.0000002835 0.68377 46.9697
174 4IGQ THR M3L GLN 0.000000014 0.72778 47.5
175 4IGQ OGA 0.0000000004152 0.66734 47.5
Feedback