Receptor
PDB id Resolution Class Description Source Keywords
2FDK 2.3 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2-OXOGLUTA METHYLATED TRINUCLEOTIDE T-MEA-T (AIR 9 DAYS) ESCHERICHIA COLI K12 BETA JELLYROLL STRUCTURAL GENOMICS PSI PROTEIN STRUCTURE INITIATIVE NORTHEAST STRUCTURAL GENOMICS CONSORTIUM NESGOXIDOREDUCTASE-DNA COMPLEX
Ref.: CRYSTAL STRUCTURES OF CATALYTIC COMPLEXES OF THE OX DNA/RNA REPAIR ENZYME ALKB. NATURE V. 439 879 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:400;
Valid;
none;
submit data
146.098 C5 H6 O5 C(CC(...
DT MA7 DT B:501;
Valid;
none;
submit data
949.61 n/a [P+](...
FE2 A:300;
Part of Protein;
none;
submit data
55.845 Fe [Fe+2...
SIN A:401;
Valid;
none;
submit data
116.072 C4 H6 O4 O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RFR 1.5 Å EC: 1.14.11.- COMPLEX STRUCTURE OF ALKB/RHEIN ESCHERICHIA COLI PROTEIN-INHIBITOR COMPLEX DEMETHYLATION ALKB FAMILY JELLYFOLD DEMETHYLASE NUCLEIC ACID BINDING NUCLEUS OXIDOREDUINHIBITOR COMPLEX
Ref.: RHEIN INHIBITS ALKB REPAIR ENZYMES AND SENSITIZES C METHYLATED DNA DAMAGE. J.BIOL.CHEM. V. 291 11083 2016
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 3T4V ic50 = 0.5 uM MD3 C16 H15 N O5 S c1ccc2cc(c....
2 3T4H ic50 = 5.2 uM MD5 C12 H12 N2 O7 S c1cc(cc(c1....
3 2FD8 - DT MA7 DT n/a n/a
4 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
5 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
6 2FDF - DT MA7 DT n/a n/a
7 2FDH - DT MA7 DT n/a n/a
8 3I2O - DT MA7 DT n/a n/a
9 2FDK - DT MA7 DT n/a n/a
10 2FDG - SIN C4 H6 O4 O=C([O-])C....
11 3I49 - DT ME6 DT n/a n/a
12 2FDJ - SIN C4 H6 O4 O=C([O-])C....
13 3I3M - DT ME6 DT n/a n/a
14 2FDI - DT MA7 DT n/a n/a
15 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(c....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3T4V ic50 = 0.5 uM MD3 C16 H15 N O5 S c1ccc2cc(c....
2 3T4H ic50 = 5.2 uM MD5 C12 H12 N2 O7 S c1cc(cc(c1....
3 2FD8 - DT MA7 DT n/a n/a
4 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
5 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
6 2FDF - DT MA7 DT n/a n/a
7 2FDH - DT MA7 DT n/a n/a
8 3I2O - DT MA7 DT n/a n/a
9 2FDK - DT MA7 DT n/a n/a
10 2FDG - SIN C4 H6 O4 O=C([O-])C....
11 3I49 - DT ME6 DT n/a n/a
12 2FDJ - SIN C4 H6 O4 O=C([O-])C....
13 3I3M - DT ME6 DT n/a n/a
14 2FDI - DT MA7 DT n/a n/a
15 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(c....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 3T4V ic50 = 0.5 uM MD3 C16 H15 N O5 S c1ccc2cc(c....
2 3T4H ic50 = 5.2 uM MD5 C12 H12 N2 O7 S c1cc(cc(c1....
3 2FD8 - DT MA7 DT n/a n/a
4 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
5 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
6 2FDF - DT MA7 DT n/a n/a
7 2FDH - DT MA7 DT n/a n/a
8 3I2O - DT MA7 DT n/a n/a
9 2FDK - DT MA7 DT n/a n/a
10 2FDG - SIN C4 H6 O4 O=C([O-])C....
11 3I49 - DT ME6 DT n/a n/a
12 2FDJ - SIN C4 H6 O4 O=C([O-])C....
13 3I3M - DT ME6 DT n/a n/a
14 2FDI - DT MA7 DT n/a n/a
15 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(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
Ligand no: 2; Ligand: DT MA7 DT; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 DT MA7 DT 1 1
2 DT ME6 DT 0.606061 0.91358
3 DT DT PST 0.6 0.833333
4 DT DT DT DT DT 0.576 0.843373
5 DG DT DC 0.565517 0.908046
6 DA DT DA DA 0.55102 0.904762
7 DC DG DT DA 0.538922 0.918605
8 DT DA DC DG 0.532934 0.918605
9 DT DT DT 0.5 0.829268
10 DC DC DT DG 0.496296 0.841463
11 DG DC 0.467532 0.872093
12 DC DG DA DC 0.466258 0.872093
13 DU DU DU DU BRU DG DU 0.444444 0.855556
14 3PD UM3 0.433333 0.860465
15 TMP 0.42623 0.807229
16 TYD 0.420635 0.797619
17 DG DA DC DG 0.418605 0.873563
18 DU DU DU DU BRU DU DU 0.417808 0.77907
19 DA DC DG DA 0.416185 0.873563
20 4TA 0.415584 0.894118
21 DG DG 0.411348 0.83908
22 PAX 0.409938 0.872093
23 DC DG 0.4 0.883721
Ligand no: 3; Ligand: SIN; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 SIN 1 1
2 MLI 0.5 0.785714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RFR; Ligand: RHN; Similar sites found: 156
This union binding pocket(no: 1) in the query (biounit: 4rfr.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.000514 0.44888 None
2 1MDC PLM 0.001887 0.43042 None
3 2HZQ STR 0.01043 0.42204 None
4 4ZU5 THM 0.002987 0.40781 None
5 4JH6 FCN 0.01481 0.40776 None
6 5T7I LAT NAG GAL 0.001907 0.46032 1.29032
7 4JGP PYR 0.005925 0.43422 1.47783
8 4IAW LIZ 0.002272 0.44295 1.59574
9 2GC0 PAN 0.003013 0.41969 1.59574
10 2JIG PD2 0.000004417 0.58215 1.97044
11 5L9V OGA 0.00003069 0.53304 1.97044
12 5L9B AKG 0.00005235 0.52186 1.97044
13 1Y7P RIP 0.00007972 0.51248 1.97044
14 4JZR 4JR 0.0004064 0.48509 1.97044
15 1X7D ORN 0.01626 0.40688 1.97044
16 1OGX EQU 0.003752 0.42351 2.29008
17 3NX2 FER 0.007811 0.41757 2.38095
18 5EPA AKG 0.000006199 0.58383 2.46305
19 4L4J NAG NAG BMA MAN NAG 0.0001412 0.52401 2.46305
20 3W21 AKG 0.0001418 0.51162 2.46305
21 2FCU AKG 0.0000001773 0.50733 2.46305
22 4D52 GIV 0.006383 0.43273 2.46305
23 4MLO PAM 0.0007643 0.42644 2.46305
24 4OMJ 2TX 0.00872 0.41392 2.46305
25 2PUL ACP 0.006939 0.40739 2.46305
26 1I7E IBS 0.03029 0.40064 2.46305
27 5FLJ QUE 0.008491 0.40014 2.68817
28 5EOB 5QQ 0.0132 0.42244 2.95567
29 3W68 PBU 0.01569 0.41149 2.95567
30 3W68 VIV 0.002521 0.40198 2.95567
31 3KFF XBT 0.00132 0.46563 3.08642
32 3KFF ZBT 0.00132 0.46563 3.08642
33 2AGC DAO 0.003023 0.44199 3.08642
34 1I06 TZL 0.00658 0.43017 3.33333
35 2ZHL NAG GAL GAL NAG 0.005797 0.41894 3.37838
36 3A76 SPD 0.01665 0.41072 3.40909
37 4Y3O OGA 0.000001315 0.63122 3.44828
38 4XCB AKG 0.000008258 0.5775 3.44828
39 4XAC AKG 0.00001647 0.56628 3.44828
40 1OS7 TAU 0.0001656 0.46211 3.44828
41 1OS7 AKG 0.0001656 0.46211 3.44828
42 4CCK OGA 0.000001911 0.45614 3.44828
43 2AXR ABL 0.007737 0.42843 3.44828
44 4YRD 3IT 0.005912 0.42799 3.44828
45 4XCB HY0 0.000245 0.42215 3.44828
46 4DE9 VTP 0.01117 0.40655 3.44828
47 4HN1 TYD 0.005539 0.42428 3.48259
48 5JSP DQY 0.01843 0.40539 3.48259
49 1NYW DAU 0.005727 0.40391 3.5533
50 4H6B 10Y 0.0111 0.40968 3.58974
51 4NG2 OHN 0.002537 0.41258 3.80435
52 3QP8 HL0 0.005948 0.4104 3.80435
53 1LFO OLA 0.004519 0.40833 3.90625
54 5LUN OGA 0.0000004468 0.6418 3.94089
55 5HV0 AKG 0.00001863 0.49104 3.94089
56 3Q8G PEE 0.002291 0.4599 3.94089
57 5LUN ARG 0.00002143 0.45983 3.94089
58 3N9Q OGA 0.002536 0.45114 3.94089
59 3N9O OGA 0.002545 0.45094 3.94089
60 3PUR 2HG 0.004457 0.43994 3.94089
61 5AB1 BCD TA5 HP6 MAN 0.01824 0.40571 3.94089
62 4FFG LBS 0.01149 0.40446 3.94089
63 4XOE KGM 0.0237 0.40244 3.94089
64 3EMZ HXH 0.02382 0.40162 3.94089
65 4QM9 CYS 0.007623 0.42828 4.04624
66 4ZSI 4R1 0.002075 0.43095 4.09357
67 4GGZ BTN 0.009906 0.40796 4.34783
68 4M26 AKG 0.0008555 0.4783 4.4335
69 3H7J PPY 0.0002913 0.47448 4.4335
70 3KV5 OGA 0.003855 0.44251 4.4335
71 3HX3 RET 0.001789 0.42964 4.4335
72 2VFT SOR 0.006632 0.4205 4.4335
73 4ZXA H8N 0.01215 0.41202 4.4335
74 1NSZ GLC 0.01403 0.40893 4.4335
75 3FW9 SLX 0.00498 0.40652 4.4335
76 3GXO MQA 0.01611 0.40594 4.4335
77 1ZP9 ATP 0.009371 0.4052 4.4335
78 3QRC SCR 0.000471 0.48453 4.4586
79 2YMZ LAT 0.001425 0.43864 4.61538
80 1SN0 T44 0.007127 0.41471 4.61538
81 4QXB OGA 0.00112 0.46333 4.92611
82 2RDQ AKG 0.0002592 0.44719 4.92611
83 1W3T 3GR 0.01133 0.41153 4.92611
84 5ML3 DL3 0.01607 0.4061 5.36913
85 5C3R AKG 0.00004035 0.50188 5.41872
86 5C3R HMU 0.00004035 0.50188 5.41872
87 5UQD AKG 0.006512 0.4283 5.41872
88 5IQT AKG 0.003472 0.40789 5.41872
89 5L8N 6RQ 0.007446 0.42993 5.46875
90 3FW4 CAQ 0.007092 0.40847 5.61798
91 3OPT AKG 0.000741 0.48073 5.91133
92 2OS2 OGA 0.001066 0.47191 5.91133
93 2YBP 2HG 0.001399 0.46566 5.91133
94 1ODM ASV 0.001583 0.43727 5.91133
95 4IGQ THR M3L GLN 0.001058 0.43542 5.91133
96 5X7Q GLC GLC GLC GLC GLC 0.01114 0.42829 5.91133
97 5X7Q GLC GLC GLC GLC 0.0128 0.42381 5.91133
98 5F3I 5UJ 0.02103 0.41336 5.91133
99 4IGQ OGA 0.00001378 0.40827 5.91133
100 3MTX PGT 0.001922 0.44254 5.96026
101 1N5S ADL 0.0007497 0.4508 6.25
102 1J3R 6PG 0.00199 0.44573 6.31579
103 1DZK PRZ 0.005991 0.41416 6.36943
104 5KEW 6SB 0.01099 0.4142 6.38298
105 1JL0 PUT 0.0002685 0.49988 6.40394
106 1Z03 OCH 0.007692 0.42671 6.40394
107 5M0T AKG 0.007991 0.42406 6.40394
108 2A1X AKG 0.00004128 0.40027 6.40394
109 5FU3 BGC BGC BGC 0.01824 0.40916 6.60377
110 4CPB GAL CN8 0.01837 0.40679 6.61157
111 5DG2 GAL GLC 0.002346 0.43608 6.66667
112 1A78 TDG 0.001119 0.47451 6.71642
113 3VV1 GAL FUC 0.004376 0.44227 6.875
114 4GJY OGA 0.0000132 0.5728 6.89655
115 5V1B 8UY 0.0008224 0.47607 6.89655
116 3RGA LSB 0.001724 0.43457 6.89655
117 2XMY CDK 0.02253 0.41723 6.89655
118 4WVW SLT 0.0001713 0.51417 6.94444
119 5I0U DCY 0.001047 0.41289 7
120 5AIG VPR 0.00384 0.43196 7.2
121 3LXI CAM 0.02458 0.4017 7.38916
122 4J25 OGA 0.000003486 0.60116 7.42358
123 1I7M PUT 0.00043 0.49211 7.88177
124 5BVB DOG 0.01176 0.41893 8.33333
125 1GP6 SIN 0.00007713 0.44614 8.37438
126 1GP6 DH2 0.00007713 0.44614 8.37438
127 1GP6 QUE 0.0000853 0.4382 8.37438
128 2GQS ADP 0.008657 0.40307 8.37438
129 5D3X 4IP 0.01037 0.4305 8.38323
130 5C5T AKG 0.00001203 0.56065 8.86699
131 4Y24 TD2 0.008013 0.41653 9.74026
132 4U0W 16G 0.007892 0.40131 9.85222
133 3G08 FEE 0.02179 0.41261 10.101
134 2BYC FMN 0.008777 0.40652 10.219
135 5H9Q TD2 0.003112 0.44149 10.3226
136 5TVM PUT 0.009993 0.42162 10.5882
137 3PUA OGA 0.002457 0.4523 10.8374
138 3KV4 OGA 0.006703 0.43127 10.8374
139 2D6M LBT 0.007035 0.41694 11.3208
140 5TFZ 7BC 0.003071 0.44165 11.3333
141 4ZU4 4TG 0.0005136 0.45817 11.4865
142 4XT2 43L 0.000993 0.41263 12.3967
143 3OYW TDG 0.00436 0.43926 12.6866
144 1GZW GAL BGC 0.005731 0.4316 12.6866
145 1W6O LAT 0.008447 0.41842 12.6866
146 3PE2 E1B 0.02016 0.40801 12.8079
147 2WMC MGP 0.01295 0.4199 12.9213
148 2OVW CBI 0.0198 0.40147 14.7783
149 1OIJ AKG 0.00001779 0.56032 15.7635
150 3WV6 GAL GLC 0.0009894 0.45848 17.734
151 3WV6 GAL BGC 0.003693 0.43557 17.734
152 2OVD DAO 0.01171 0.41977 20.8791
153 4UEC MGT 0.01582 0.4154 24.359
154 2QX0 PH2 0.01521 0.4138 24.5283
155 1QKQ MAN 0.002596 0.43288 26.0563
156 2XUM OGA 0.00002617 0.55758 35
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