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Receptor
PDB id Resolution Class Description Source Keywords
4IGQ 2.35 Å NON-ENZYME: OTHER HISTONE H3 LYSINE 4 DEMETHYLATING RICE JMJ703 IN COMPLEX WIT METHYLATED H3K4 SUBSTRATE ORYZA SATIVA JAPONICA GROUP JUMONJIC HISTONE DEMETHYLASE STRUCTURAL PROTEIN-TRANSCRIPTCOMPLEX
Ref.: STRUCTURAL BASIS OF A HISTONE H3 LYSINE 4 DEMETHYLA REQUIRED FOR STEM ELONGATION IN RICE. PLOS GENET. V. 9 03239 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:501;
Part of Protein;
none;
submit data
55.845 Fe [Fe+3...
OGA A:502;
Valid;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
THR M3L GLN B:3;
Valid;
none;
submit data
403.524 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4IGQ 2.35 Å NON-ENZYME: OTHER HISTONE H3 LYSINE 4 DEMETHYLATING RICE JMJ703 IN COMPLEX WIT METHYLATED H3K4 SUBSTRATE ORYZA SATIVA JAPONICA GROUP JUMONJIC HISTONE DEMETHYLASE STRUCTURAL PROTEIN-TRANSCRIPTCOMPLEX
Ref.: STRUCTURAL BASIS OF A HISTONE H3 LYSINE 4 DEMETHYLA REQUIRED FOR STEM ELONGATION IN RICE. PLOS GENET. V. 9 03239 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
2 4IGO - AKG C5 H6 O5 C(CC(=O)O)....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
2 4IGO - AKG C5 H6 O5 C(CC(=O)O)....
50% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
2 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
3 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
4 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
5 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
6 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
7 6DQ5 Kd = 6 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
8 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
9 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
10 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
11 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
12 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
13 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
14 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
15 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
16 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
17 6DQ6 Kd = 9 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
18 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
19 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
20 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
21 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
22 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
23 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
24 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
25 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
26 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
27 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
28 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
29 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
30 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
31 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
32 5FPL - MN QAY n/a n/a
33 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
34 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
35 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
36 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
37 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
38 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
39 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
40 4IGO - AKG C5 H6 O5 C(CC(=O)O)....
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
Ligand no: 2; Ligand: THR M3L GLN; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 THR M3L GLN 1 1
2 ALA ARG M3L SER 0.493976 0.790323
3 ALA ARG THR LYS GLN THR ALA ARG 0.488889 0.672131
4 THR ALA ARG M3L SER THR 0.487805 0.790323
5 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.473118 0.819672
6 GLN THR ALA ARG M3L SER 0.460784 0.854839
7 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.460674 0.655738
8 ALA ARG THR M3L GLN THR ALA 0.447917 0.868852
9 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.447917 0.868852
10 ALA ARG THR M3L GLN THR ALA ARG LYS 0.443299 0.868852
11 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.443299 0.868852
12 ALA ALA THR M3L GLN THR ALA ARG 0.419753 0.981132
13 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.417476 0.852459
14 LYS GLN THR ALA ARG M3L SER THR GLY 0.407767 0.854839
15 ASN LEU LEU GLN LYS LYS 0.406593 0.696429
16 ASP PHE M3L THR ASP 0.405941 0.913793
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IGQ; Ligand: THR M3L GLN; Similar sites found with APoc: 182
This union binding pocket(no: 1) in the query (biounit: 4igq.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5MU6 MYA 1.66667
2 5MU6 KFK 1.66667
3 5TUF TDC 1.66667
4 2XCG XCG 1.66667
5 5H9Y BGC BGC BGC BGC BGC 1.66667
6 1OFL ASG GCD 1.66667
7 2RDQ AKG 1.73611
8 1OJK GLC BGC 1.94444
9 4FFG 0U8 1.94444
10 3ZDS HMQ 1.94444
11 5JWP AKG 1.98864
12 2Y0I AKG 1.98864
13 1H2K OGA 2.00573
14 2XUM OGA 2.00573
15 3P3N AKG 2.00573
16 4B7E OGA 2.00573
17 2WA4 069 2.00573
18 1H2M OGA 2.00573
19 5C3R AKG 2.04082
20 5C3R HMU 2.04082
21 4LIT AKG 2.22222
22 2RKV ZBA 2.22222
23 3KV4 OGA 2.22222
24 1ZB6 GST 2.28013
25 4OJ8 AKG 2.38908
26 4OJ8 2TQ 2.38908
27 1PIG BGC 2.5
28 5X7Q GLC GLC 2.5
29 2X1E X1E 2.52101
30 1J3R 6PG 2.63158
31 2GC0 PAN 2.65957
32 4IE6 UN9 2.77778
33 2A1X AKG 2.92208
34 2VL1 GLY GLY 3.05556
35 2YNE NHW 3.05556
36 2YNE YNE 3.05556
37 5O9W AKG 3.05556
38 5M90 JIF 3.05556
39 4Q0P 0MK 3.07692
40 3WW2 LPK 3.125
41 3WW2 SF6 3.125
42 2HRL SIA GAL SIA BGC NGA CEQ 3.14961
43 5OCG 9R5 3.1746
44 5TFZ 7BC 3.33333
45 1GP6 SIN 3.37079
46 1GP6 DH2 3.37079
47 1GP6 QUE 3.37079
48 1DRY AAG 3.39506
49 1DRY AKG 3.39506
50 4XCB AKG 3.44828
51 6FA4 D1W 3.46821
52 1RV1 IMZ 3.52941
53 4OCT AKG 3.6036
54 4YVN EBS 3.61111
55 4UWJ 7L5 3.61111
56 4UWJ MYA 3.61111
57 3M3E GAL A2G NPO 3.72671
58 2J5B TYE 3.73563
59 2D6M LBT 3.77358
60 5FUI APY 3.78788
61 1OS7 TAU 3.88693
62 1OS7 AKG 3.88693
63 5XEG AKG 3.8961
64 2JIG PD2 4.01786
65 5EW9 5VC 4.05904
66 1GPM AMP 4.16667
67 3NZ1 3NY 4.21456
68 1TT8 PHB 4.26829
69 1LRH NLA 4.29448
70 4OIT MAN 4.42478
71 5JSP DQY 4.47761
72 1A78 TDG 4.47761
73 2Y88 2ER 4.5082
74 4BG1 OGA 4.72222
75 4BG1 IVL 4.72222
76 3HQP OXL 5
77 5LDQ NAP 5.08475
78 4QM9 CYS 5.20231
79 5CX6 CDP 5.27778
80 1SDW IYT 5.41401
81 2FCU AKG 5.43131
82 1UNB AKG 5.46624
83 1UNB PN1 5.46624
84 4BXF AKG 5.55556
85 5L2R MLA 5.55556
86 4NPL AKG 5.6
87 1QKQ MAN 5.6338
88 6D61 4AA 5.64103
89 4NAO AKG 5.82822
90 4PTN PYR 5.8309
91 4Y3O OGA 5.83333
92 5Y4K AKR 5.83333
93 5TZO 7V7 5.85106
94 4RFR RHN 5.91133
95 6FXR AKG 6.11111
96 1RYD GLC 6.11111
97 3CM2 X23 6.15385
98 4HSJ 6PC 6.32184
99 4D4U FUC NDG GAL FUC 6.34921
100 1LSH PLD 6.38889
101 4M26 AKG 6.38889
102 5HV0 AKG 6.45161
103 1SLT NDG GAL 6.71642
104 2IUW AKG 6.72269
105 6EWZ APC 6.75105
106 5M6N 7H9 6.77966
107 3HCH RSM 6.84932
108 5ZM4 9FU 6.86275
109 5ZM4 AKG 6.86275
110 3UW5 MAA CHG PRO 0DQ 6.89655
111 5KJW 53C 6.94444
112 5I0U DCY 7
113 5A5W GUO 7.11462
114 4LUT DCS 7.22222
115 5EIN NAP 7.40741
116 5C5T AKG 7.45614
117 2RG0 CBI 7.5
118 4CCK OGA 8.05556
119 6GNO XDI 8.14815
120 5Y4R C2E 8.27586
121 3DLG GWE 8.33333
122 3WG3 A2G GAL NAG FUC 8.42697
123 1USF NAP 8.42697
124 3UW4 MAA CHG PRO 0DQ 8.69565
125 4QXB OGA 8.82353
126 1F9V ADP 8.93372
127 6F4T OGA 9.01961
128 5XLY C2E 9.02256
129 1WW5 SGA BGC 9.375
130 6E1Q CFA 9.44444
131 4MTI 2DX 9.56522
132 1MEX RAC 9.85915
133 4CCO OGA 10
134 1KJ1 MAN 10.0917
135 2V92 ATP 10.3448
136 1UYY BGC BGC 10.687
137 5ZMY TAR 10.828
138 5OQW A4E 11.0236
139 1ZZ7 S0H 11.1111
140 3SCH TB6 11.1111
141 5FLJ QUE 11.828
142 3DZ6 PUT 11.9403
143 1I7M CG 11.9403
144 6F6D AKG 12.5
145 5FP3 3JI 12.5
146 1OPB RET 12.6866
147 5TVF CGQ 12.9412
148 1QFY FAD 12.987
149 1QFY NAP 12.987
150 3AVR OGA 13.0556
151 6FUL E7Z 13.0556
152 4UF0 MMK 13.3333
153 3PUR 2HG 13.6111
154 3N9Q OGA 13.6111
155 3N9O OGA 13.6111
156 4CCN OGA 14.2857
157 2Z49 AMG 15
158 4F7E 0SH 15.3061
159 3U6W KIV 15.8333
160 3IWD M2T 16.1765
161 4QYN RTL 16.5414
162 1OIK AKG 16.9435
163 1OIK C26 16.9435
164 1OIJ AKG 16.9435
165 3N9P OGA 18.75
166 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 26.3158
167 4WO4 JLS 30
168 5U98 1KX 30.303
169 5WL1 CUY 30.303
170 5WL1 D3D 30.303
171 5KR7 6X9 41.1111
172 2YBP 2HG 41.3889
173 5FWE OGA 41.3889
174 6H8P OGA 41.3889
175 5LY1 PPI 41.3889
176 5F3I 5UJ 41.3889
177 5LY2 OGA 41.3889
178 2Q8E OGA 42.3295
179 2P5B OGA 42.3295
180 5FP4 YC8 44.012
181 2OS2 OGA 45.4545
182 3OPT AKG 47.5
Pocket No.: 2; Query (leader) PDB : 4IGQ; Ligand: OGA; Similar sites found with APoc: 145
This union binding pocket(no: 2) in the query (biounit: 4igq.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 6F6J CUW 1.39665
2 6F6J SIN 1.39665
3 2RDQ AKG 1.73611
4 3ZDS HMQ 1.94444
5 5WZN A2G 1.94444
6 3ZDS M8O 1.94444
7 3ZDS OMD 1.94444
8 3ZDS HQ9 1.94444
9 3WCA FPS 1.94444
10 5JWP AKG 1.98864
11 2Y0I AKG 1.98864
12 1H2M OGA 2.00573
13 2WA4 069 2.00573
14 1H2K OGA 2.00573
15 2XUM OGA 2.00573
16 3P3N AKG 2.00573
17 4B7E OGA 2.00573
18 5B4B LP5 2.01613
19 1NYW DAU 2.03046
20 5C3R AKG 2.04082
21 5C3R HMU 2.04082
22 5Y72 DST 2.08955
23 1ODM ASV 2.1148
24 4LIT AKG 2.22222
25 6EXF LYS 2.22222
26 1OLM VTQ 2.22222
27 3KV4 OGA 2.22222
28 6ES9 FAD 2.22222
29 5DV2 C5P 2.22222
30 5YBL AKG 2.2293
31 6CZ3 FLJ 2.27273
32 4OJ8 AKG 2.38908
33 4P7X AKG 2.39726
34 4P7X YCP 2.39726
35 1NX4 AKG 2.5641
36 5NCJ SIN 2.61194
37 5NCJ HL5 2.61194
38 4AT3 LTI 2.67559
39 4IE6 UN9 2.77778
40 2Q7D ANP 2.89017
41 5DXI TRE 2.98013
42 5O9W AKG 3.05556
43 5U23 TQP 3.05556
44 4Q0P 0MK 3.07692
45 3WW2 SF6 3.125
46 3WW2 LPK 3.125
47 6EOZ 58K 3.24675
48 6EOZ AKG 3.24675
49 5TFZ 7BC 3.33333
50 5VLC HSO 3.33333
51 3N0Y APC 3.35196
52 1GP6 SIN 3.37079
53 1GP6 DH2 3.37079
54 1GP6 QUE 3.37079
55 4XCB HY0 3.44828
56 4XCB AKG 3.44828
57 4OCT AKG 3.6036
58 2QF7 AGS 3.61111
59 4JZR 4JR 3.7037
60 1OS7 TAU 3.88693
61 1OS7 AKG 3.88693
62 5XEG AKG 3.8961
63 2HFN FMN 3.92157
64 2JIG PD2 4.01786
65 3B99 U51 4.16667
66 1LRH NLA 4.29448
67 5OX6 A1Z 4.36508
68 2WBP ZZU 4.46927
69 2WBP SIN 4.46927
70 2ET1 GLV 4.47761
71 5JSP DQY 4.47761
72 1WBI BTN 4.65116
73 4BG1 OGA 4.72222
74 4BG1 IVL 4.72222
75 1Y52 BTN 4.7619
76 1GT4 UNA 5.03145
77 4QM9 CYS 5.20231
78 1WLE SRP 5.27778
79 2FCU AKG 5.43131
80 1UNB AKG 5.46624
81 1UNB PN1 5.46624
82 3BIY 01K 5.52632
83 4BXF AKG 5.55556
84 1X0P FAD 5.59441
85 4NPL AKG 5.6
86 1ZP9 ATP 5.81395
87 4NAO AKG 5.82822
88 4Y3O OGA 5.83333
89 4RFR RHN 5.91133
90 1UZD CAP 5.97015
91 1Q6O LG6 6.01852
92 6FXR AKG 6.11111
93 4HSJ 6PC 6.32184
94 4M26 ZZU 6.38889
95 4M26 AKG 6.38889
96 4M26 SIN 6.38889
97 4EI7 GDP 6.38889
98 5HV0 AKG 6.45161
99 2IUW AKG 6.72269
100 5ZM4 9FU 6.86275
101 5ZM4 AKG 6.86275
102 5I0U DCY 7
103 4ZXA H8N 7.14286
104 3TTN SPD 7.35294
105 5C5T AKG 7.45614
106 2RFZ CTR 7.5
107 4CCK OGA 8.05556
108 5T2U NAP 8.06452
109 2ARC ARA 8.53659
110 4QXB OGA 8.82353
111 3WR7 COA 8.82353
112 1NKI PPF 8.88889
113 6F4T OGA 9.01961
114 4K3H 1OM 9.32203
115 1MJJ HAL 9.58904
116 3E2M E2M 9.72973
117 1MEX RAC 9.85915
118 4CCO OGA 10
119 3MPB FRU 10.9756
120 5FLJ QUE 11.828
121 6F6D AKG 12.5
122 5FP3 3JI 12.5
123 3AVR OGA 13.0556
124 6FUL E7Z 13.0556
125 4UF0 MMK 13.3333
126 3PUR 2HG 13.6111
127 3N9O OGA 13.6111
128 3N9Q OGA 13.6111
129 4CCN OGA 14.2857
130 1OIK C26 16.9435
131 1OIK AKG 16.9435
132 1OIJ AKG 16.9435
133 3N9P OGA 18.75
134 2IYG FMN 21.7742
135 5KR7 6X9 41.1111
136 5LY2 OGA 41.3889
137 5F3I 5UJ 41.3889
138 5FWE OGA 41.3889
139 2YBP 2HG 41.3889
140 6H8P OGA 41.3889
141 2Q8E OGA 42.3295
142 2P5B OGA 42.3295
143 5FP4 YC8 44.012
144 2OS2 OGA 45.4545
145 3OPT AKG 47.5
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