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 1256 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 1068 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 (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 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 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
4 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
5 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
6 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
7 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
8 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
9 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
10 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
11 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
12 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
13 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
14 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
15 5FPL - MN QAY n/a n/a
16 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
17 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
18 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
19 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
20 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
21 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
22 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
23 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: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 THR M3L GLN 1 1
2 THR ALA ARG M3L SER THR 0.5 0.790323
3 ALA ARG M3L SER 0.488095 0.790323
4 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.442105 0.819672
5 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.438776 0.868852
6 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.438776 0.868852
7 ALA ARG THR M3L GLN THR ALA 0.438776 0.868852
8 ALA ARG THR M3L GLN THR ALA ARG LYS 0.434343 0.868852
9 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.428571 0.655738
10 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.424779 0.868852
11 LYS GLN THR ALA ARG M3L SER THR GLY 0.413462 0.854839
12 ASP PHE M3L THR ASP 0.401961 0.896552
13 ASN LEU LEU GLN LYS LYS 0.4 0.690909
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: 105
This union binding pocket(no: 1) in the query (biounit: 4igq.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5H9Y BGC BGC BGC BGC BGC 0.02215 0.40323 1.66667
2 2RDQ AKG 0.002812 0.40546 1.73611
3 3ZDS HQ9 0.02038 0.40574 1.94444
4 4FFG 0U8 0.0205 0.40497 1.94444
5 3ZDS HMQ 0.01794 0.40361 1.94444
6 2Y0I AKG 0.00004823 0.54259 1.98864
7 1H2K OGA 0.00001737 0.56749 2.00573
8 1H2M OGA 0.00001779 0.56679 2.00573
9 2XUM OGA 0.00001967 0.56425 2.00573
10 3P3N AKG 0.00002635 0.55695 2.00573
11 4B7E OGA 0.00004195 0.54603 2.00573
12 2WA4 069 0.0000466 0.51746 2.00573
13 5C3R AKG 0.000311 0.46298 2.04082
14 5C3R HMU 0.000311 0.46298 2.04082
15 4LIT AKG 0.000006176 0.45754 2.22222
16 3KV4 OGA 0.01768 0.40865 2.22222
17 4OJ8 AKG 0.0007283 0.43528 2.38908
18 1PIG BGC 0.0001987 0.43479 2.5
19 5X7Q GLC GLC 0.005592 0.4244 2.5
20 2X1E X1E 0.01506 0.41255 2.52101
21 1J3R 6PG 0.00131 0.40712 2.63158
22 2GC0 PAN 0.004401 0.41246 2.65957
23 4DSU BZI 0.007202 0.42799 3.1746
24 5TFZ 7BC 0.001952 0.45139 3.33333
25 1GP6 QUE 0.0004925 0.46143 3.37079
26 1GP6 SIN 0.0004492 0.46143 3.37079
27 1GP6 DH2 0.0004492 0.41759 3.37079
28 4XCB AKG 0.006046 0.43204 3.44828
29 4OCT AKG 0.001832 0.44746 3.6036
30 4YVN EBS 0.002891 0.45221 3.61111
31 3M3E GAL A2G NPO 0.0053 0.43045 3.72671
32 2D6M LBT 0.003495 0.43111 3.77358
33 5FUI APY 0.00004691 0.53959 3.78788
34 1OS7 AKG 0.001117 0.42726 3.88693
35 1OS7 TAU 0.001117 0.42726 3.88693
36 2JIG PD2 0.0002127 0.42318 4.01786
37 1GPM AMP 0.02353 0.40745 4.16667
38 3NZ1 3NY 0.007262 0.42562 4.21456
39 4GJY OGA 0.000001093 0.63417 4.25532
40 5JSP DQY 0.0008608 0.47682 4.47761
41 2ET1 GLV 0.001629 0.4631 4.47761
42 1A78 TDG 0.01587 0.40063 4.47761
43 5LDQ NAP 0.02572 0.40321 5.08475
44 4QM9 CYS 0.002169 0.45729 5.20231
45 1SDW IYT 0.01359 0.40147 5.41401
46 2FCU AKG 0.003427 0.44666 5.43131
47 4BXF AKG 0.00006851 0.53544 5.55556
48 5L2R MLA 0.01899 0.40307 5.55556
49 1X9Q FLU 0.01165 0.41294 5.59701
50 4NPL AKG 0.001127 0.47222 5.6
51 1QKQ MAN 0.0004342 0.50309 5.6338
52 4NAO AKG 0.02022 0.41235 5.82822
53 4PTN PYR 0.02017 0.40996 5.8309
54 4Y3O OGA 0.00002362 0.56053 5.83333
55 4RFR RHN 0.001058 0.43542 5.91133
56 1RYD GLC 0.0229 0.40782 6.11111
57 3CM2 X23 0.007617 0.43064 6.15385
58 4D4U FUC NDG GAL FUC 0.02538 0.4008 6.34921
59 5HV0 AKG 0.0002313 0.47908 6.45161
60 1SLT NDG GAL 0.01559 0.40279 6.71642
61 2IUW AKG 0.003933 0.43633 6.72269
62 5M6N 7H9 0.01118 0.42169 6.77966
63 3HCH RSM 0.01794 0.40962 6.84932
64 5KJW 53C 0.001505 0.46295 6.94444
65 5I0U DCY 0.0003905 0.47982 7
66 2WZ5 MET 0.00004365 0.51979 7.18954
67 5C5T AKG 0.001892 0.45206 7.45614
68 1Y9Q MED 0.009681 0.42375 7.8125
69 4CCK OGA 0.00001885 0.56644 8.05556
70 3WG3 A2G GAL NAG FUC 0.01766 0.40976 8.42697
71 5XLY C2E 0.007026 0.40353 9.02256
72 1WW5 SGA BGC 0.006006 0.43506 9.375
73 4MTI 2DX 0.01378 0.41747 9.56522
74 1MEX RAC 0.006167 0.42202 9.85915
75 4CCO OGA 0.0001427 0.51468 10
76 1UYY BGC BGC 0.004326 0.43943 10.687
77 1ZZ7 S0H 0.01021 0.42045 11.1111
78 5FLJ QUE 0.003251 0.40315 11.828
79 1I7M CG 0.01741 0.40019 11.9403
80 5FP3 3JI 0.000000651 0.53608 12.5
81 1OPB RET 0.004462 0.41602 12.6866
82 5TVF CGQ 0.01476 0.40782 12.9412
83 3AVS OGA 0.0000001562 0.65388 13.0556
84 3AVR OGA 0.0000004123 0.65248 13.0556
85 4UF0 MMK 0.00001862 0.47541 13.3333
86 3PUR 2HG 0.004391 0.43996 13.6111
87 3N9Q OGA 0.008521 0.41966 13.6111
88 3N9O OGA 0.009513 0.41687 13.6111
89 4CCN OGA 0.0000451 0.54447 14.2857
90 3IWD M2T 0.01547 0.40333 16.1765
91 4QYN RTL 0.008321 0.40221 16.5414
92 1OIK AKG 0.006903 0.43135 16.9435
93 1OIK C26 0.00568 0.41131 16.9435
94 3N9P OGA 0.009222 0.41783 18.75
95 5KR7 6X9 0.0000002674 0.6228 41.1111
96 2YBP 2HG 0.000000006916 0.74372 41.3889
97 5F3I 5UJ 0.000000003543 0.73962 41.3889
98 5FWE OGA 0.00000001504 0.73432 41.3889
99 5LY2 OGA 0.00000002131 0.72567 41.3889
100 5LY1 PPI 0.0000009555 0.64546 41.3889
101 2Q8E OGA 0.000000003135 0.76215 42.3295
102 2Q8C AKG 0.00000001857 0.72902 42.3295
103 2P5B OGA 0.00000001507 0.68151 42.3295
104 2OS2 OGA 0.000000003501 0.75957 45.4545
105 3OPT AKG 0.000000014 0.72778 47.5
Pocket No.: 2; Query (leader) PDB : 4IGQ; Ligand: OGA; Similar sites found: 64
This union binding pocket(no: 2) in the query (biounit: 4igq.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WCA FPS 0.01533 0.41622 1.94444
2 3ZDS HQ9 0.001595 0.40663 1.94444
3 3ZDS HMQ 0.000833 0.40361 1.94444
4 2Y0I AKG 0.00000116 0.53023 1.98864
5 1H2K OGA 0.0000006784 0.55759 2.00573
6 1H2M OGA 0.0000007417 0.55584 2.00573
7 2XUM OGA 0.0000007833 0.55454 2.00573
8 3P3N AKG 0.000001169 0.54661 2.00573
9 4B7E OGA 0.0000009865 0.53331 2.00573
10 2WA4 069 0.000002634 0.46433 2.00573
11 4LIT AKG 0.0000006076 0.61977 2.22222
12 3KV4 OGA 0.001604 0.40496 2.22222
13 4P7X AKG 0.002885 0.44606 2.39726
14 5TFZ 7BC 0.00007531 0.43679 3.33333
15 1GP6 QUE 0.0005149 0.4965 3.37079
16 1GP6 SIN 0.0004805 0.4965 3.37079
17 4OCT AKG 0.00004714 0.43566 3.6036
18 1R6W 164 0.004732 0.42321 3.72671
19 2JIG PD2 0.00001176 0.56205 4.01786
20 4GJY OGA 0.00000004418 0.61177 4.25532
21 1LRH NLA 0.002923 0.42744 4.29448
22 2ET1 GLV 0.001108 0.41317 4.47761
23 5JSP DQY 0.002329 0.40003 4.47761
24 1Y52 BTN 0.02653 0.40962 4.7619
25 4QM9 CYS 0.0009681 0.4261 5.20231
26 2FCU AKG 0.000274 0.43682 5.43131
27 3BIY 01K 0.03289 0.40372 5.52632
28 4BXF AKG 0.0000008759 0.53544 5.55556
29 1X0P FAD 0.008361 0.41987 5.59441
30 4NPL AKG 0.00007805 0.45888 5.6
31 4NAO AKG 0.005385 0.40709 5.82822
32 4Y3O OGA 0.0000005569 0.56053 5.83333
33 4RFR RHN 0.00001378 0.40827 5.91133
34 5HV0 AKG 0.000002248 0.45529 6.45161
35 2IUW AKG 0.00001636 0.46103 6.72269
36 5I0U DCY 0.000027 0.44152 7
37 4ZXA H8N 0.0006356 0.40717 7.14286
38 5C5T AKG 0.0003839 0.41373 7.45614
39 4CCK OGA 0.0000004206 0.56644 8.05556
40 4QXB OGA 0.00002926 0.52515 8.82353
41 1NKI PPF 0.003178 0.43834 8.88889
42 4CCO OGA 0.00000117 0.51468 10
43 5FP3 3JI 0.00000001548 0.4465 12.5
44 3AVR OGA 0.000000001046 0.65248 13.0556
45 3AVS OGA 0.000000001215 0.5996 13.0556
46 4UF0 MMK 0.00008609 0.53202 13.3333
47 3PUR 2HG 0.0003934 0.42954 13.6111
48 3N9O OGA 0.001007 0.41931 13.6111
49 3N9Q OGA 0.001091 0.41552 13.6111
50 4CCN OGA 0.000001245 0.54447 14.2857
51 1OIK AKG 0.0006542 0.43135 16.9435
52 1OIJ AKG 0.002498 0.41685 16.9435
53 3N9P OGA 0.000971 0.42007 18.75
54 5KR7 6X9 0.0000000001801 0.58756 41.1111
55 5F3I 5UJ 0.000000013 0.80809 41.3889
56 5FWE OGA 0.00000000005872 0.73432 41.3889
57 5LY2 OGA 0.00000000009062 0.72567 41.3889
58 2YBP 2HG 0.000000000197 0.67995 41.3889
59 5LY1 PPI 0.01221 0.40294 41.3889
60 2Q8C AKG 0.00000000007633 0.72902 42.3295
61 2Q8E OGA 0.00000000007802 0.69633 42.3295
62 2P5B OGA 0.000000000344 0.58009 42.3295
63 2OS2 OGA 0.00000000008885 0.69402 45.4545
64 3OPT AKG 0.0000000004152 0.66734 47.5
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