Receptor
PDB id Resolution Class Description Source Keywords
4NPL 1.65 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF ZEBRAFISH ALKBH5 IN COMPLEX WITH ALPHA- KETOGLUTARATE DANIO RERIO OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF THE RNA DEMETHYLASE ALKBH5 FRO ZEBRAFISH. FEBS LETT. V. 588 892 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG B:301;
A:301;
Valid;
Valid;
none;
none;
submit data
146.098 C5 H6 O5 C(CC(...
MN B:300;
A:300;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4NPL 1.65 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF ZEBRAFISH ALKBH5 IN COMPLEX WITH ALPHA- KETOGLUTARATE DANIO RERIO OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF THE RNA DEMETHYLASE ALKBH5 FRO ZEBRAFISH. FEBS LETT. V. 588 892 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 4NPL - AKG C5 H6 O5 C(CC(=O)O)....
2 4NPM - SIN C4 H6 O4 O=C([O-])C....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4O61 ic50 = 488 uM CIT C6 H8 O7 C(C(=O)O)C....
2 4OCT ic50 = 9 uM AKG C5 H6 O5 C(CC(=O)O)....
3 4NPL - AKG C5 H6 O5 C(CC(=O)O)....
4 4NPM - SIN C4 H6 O4 O=C([O-])C....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 4O61 ic50 = 488 uM CIT C6 H8 O7 C(C(=O)O)C....
2 4OCT ic50 = 9 uM AKG C5 H6 O5 C(CC(=O)O)....
3 4NPL - AKG C5 H6 O5 C(CC(=O)O)....
4 4NPM - SIN C4 H6 O4 O=C([O-])C....
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 : 4NPL; Ligand: AKG; Similar sites found: 103
This union binding pocket(no: 1) in the query (biounit: 4npl.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1A78 TDG 0.0005494 0.47856 None
2 1C1L GAL BGC 0.002298 0.44066 None
3 3PUA OGA 0.001566 0.44244 2
4 5TFZ 7BC 0.0008822 0.43732 2
5 3KV5 OGA 0.00315 0.43625 2
6 3M94 M7M 0.009414 0.40843 2.1164
7 4QYN RTL 0.01213 0.42426 2.25564
8 3PUR 2HG 0.001197 0.45077 2.4
9 3N9Q OGA 0.004714 0.42471 2.4
10 3N9P OGA 0.004635 0.42444 2.4
11 3N9O OGA 0.004773 0.42392 2.4
12 2ET1 GLV 0.0003973 0.4736 2.48756
13 3SCH TB6 0.002787 0.42025 2.52525
14 1J3R 6PG 0.004488 0.42941 2.63158
15 2JIG PD2 0.0000001728 0.64818 2.67857
16 4QDC ASD 0.009356 0.42045 2.8
17 1ZM1 BGC BGC BGC 0.01523 0.4099 2.90456
18 1Y0G 8PP 0.03765 0.41499 3.14136
19 5L9V OGA 0.000001551 0.54017 3.2
20 5L9B AKG 0.000003076 0.52967 3.2
21 4YRD 3IT 0.0001066 0.50789 3.2
22 4XCB AKG 0.000086 0.49265 3.2
23 5IQT AKG 0.0001005 0.42154 3.2
24 1GQG DCD 0.01639 0.41598 3.2
25 5LRT ADP 0.03305 0.40275 3.2
26 5IQT 6CU 0.0001897 0.40217 3.2
27 5V1B 8UY 0.0009793 0.44451 3.33333
28 1UNB AKG 0.000004022 0.40843 3.6
29 3HX3 RET 0.02501 0.40011 3.6
30 2FCU AKG 0.000002692 0.57982 4
31 5C3R AKG 0.000001492 0.48741 4
32 5C3R HMU 0.000001492 0.48741 4
33 3AGC RCC 0.02006 0.41682 4
34 1W3T 3GR 0.002909 0.41462 4
35 5F3I 5UJ 0.007169 0.46607 4.4
36 4NAO AKG 0.0005432 0.46294 4.4
37 2OS2 OGA 0.003543 0.42701 4.4
38 2YBP 2HG 0.004133 0.42359 4.4
39 3OPT AKG 0.004918 0.41956 4.4
40 3KV4 OGA 0.01174 0.40078 4.4
41 3MTX PGT 0.002398 0.47252 4.63576
42 1OIK AKG 0.00003298 0.52946 4.8
43 1OIJ AKG 0.00001688 0.50412 4.8
44 1OIK C26 0.0001706 0.42728 4.8
45 3QP8 HL0 0.01442 0.41137 4.8913
46 2OVD DAO 0.007751 0.40946 4.94506
47 5LXB 7A9 0.007233 0.41305 4.95868
48 1WW5 SGA BGC 0.007165 0.41259 5
49 4B0T ADP 0.004457 0.44969 5.2
50 3Q8G PEE 0.01593 0.44616 5.2
51 2A1X AKG 0.0001583 0.44609 5.2
52 3H7J PPY 0.001144 0.41178 5.34979
53 1KGI T4A 0.004924 0.44663 5.51181
54 3NNF AKG 0.0000009529 0.579 5.6
55 2OG7 SIN 0.0002102 0.47873 5.6
56 4IGQ THR M3L GLN 0.001127 0.47222 5.6
57 5UQD AKG 0.00075 0.46013 5.6
58 4IGQ OGA 0.00007805 0.45888 5.6
59 5M0T AKG 0.0008799 0.45641 5.6
60 4J25 OGA 0.0000007424 0.60595 5.67686
61 5C5T AKG 0.0000002447 0.58904 5.70175
62 3QRC SCR 0.00003775 0.537 5.73248
63 4ZXA H8N 0.00471 0.40586 5.95238
64 4GJY OGA 0.0001838 0.48917 5.95745
65 5I0U DCY 0.00005553 0.47677 6
66 4BVA T3 0.006422 0.45793 6
67 1H2K OGA 0.0008898 0.45296 6
68 2XUM OGA 0.001107 0.44796 6
69 1H2M OGA 0.001121 0.44752 6
70 4B7E OGA 0.001419 0.44571 6
71 3P3N AKG 0.001394 0.44442 6
72 2Y0I AKG 0.002432 0.43385 6
73 2WA4 069 0.001709 0.41545 6
74 1MEX RAC 0.01396 0.40471 6.10329
75 1GP6 SIN 0.000000223 0.6791 6.4
76 1GP6 QUE 0.0000002482 0.6791 6.4
77 4CCN OGA 0.00009357 0.50518 6.4
78 4CCK OGA 0.000169 0.49034 6.4
79 1GP6 DH2 0.000000223 0.45446 6.4
80 4UEC MGT 0.01197 0.40732 7.06522
81 5LUN OGA 0.000000159 0.6181 7.6
82 4Y3O OGA 0.0001212 0.498 7.6
83 5LUN ARG 0.000001206 0.43517 7.6
84 4L4J NAG NAG BMA MAN NAG 0.001566 0.45224 8.1448
85 3OYW TDG 0.00847 0.40012 9.70149
86 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.0003193 0.41106 9.73451
87 3WV6 GAL GLC 0.0004083 0.45808 10
88 4JZR 4JR 0.00003759 0.49457 10.6481
89 4XAC AKG 0.000008132 0.55594 10.8
90 1OS7 AKG 0.00006839 0.42213 10.8
91 1OS7 TAU 0.00006839 0.42213 10.8
92 5HV0 AKG 0.0000001878 0.6582 11.5207
93 1NYW DAU 0.005969 0.43587 11.6751
94 5I8T LAC 0.004171 0.41528 11.7318
95 2D6M LBT 0.0001476 0.51667 11.9497
96 5EPA AKG 0.00001927 0.52181 12
97 3W21 AKG 0.000168 0.45967 12
98 4QM9 CYS 0.00009712 0.50449 12.1387
99 1NX4 AKG 0.0009046 0.45463 12.4
100 5DG2 GAL GLC 0.0001877 0.48912 14.0741
101 4M26 AKG 0.0003255 0.4772 22.4
102 4CCO OGA 0.0005313 0.45639 25
103 4QXB OGA 0.0013 0.45538 35.2941
Pocket No.: 2; Query (leader) PDB : 4NPL; Ligand: AKG; Similar sites found: 14
This union binding pocket(no: 2) in the query (biounit: 4npl.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LVG 5GP 0.01572 0.40837 1.0101
2 3KFF ZBT 0.002473 0.42513 3.08642
3 3KFF XBT 0.002473 0.42513 3.08642
4 5JSP DQY 0.003481 0.42582 3.48259
5 5YAS FAC 0.00843 0.41587 5.2
6 4WVW SLT 0.01658 0.40238 5.55556
7 2YMZ LAT 0.0001366 0.49958 6.92308
8 5T48 MGP 0.01579 0.40125 7.06522
9 2RDQ AKG 0.0003046 0.4014 7.6
10 1I82 BGC BGC 0.005189 0.4191 11.1111
11 5KEW 6SB 0.008058 0.40995 11.7021
12 4OJ8 AKG 0.000393 0.40387 12.4
13 2X4Z X4Z 0.01471 0.4335 13.6
14 3VV1 GAL FUC 0.0004269 0.43123 20
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