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Receptor
PDB id Resolution Class Description Source Keywords
4OCT 2.28 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN ALKBH5 CRYSTALLIZED IN THE PRESEN MN^{2+} AND 2-OXOGLUTARATE HOMO SAPIENS STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC RNDEMETHYLASE OXIDOREDUCTASE
Ref.: STRUCTURES OF HUMAN ALKBH5 DEMETHYLASE REVEAL A UNI BINDING MODE FOR SPECIFIC SINGLE-STRANDED N6-METHYL RNA DEMETHYLATION. J.BIOL.CHEM. V. 289 17299 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UNX B:508;
B:512;
A:506;
B:506;
A:503;
B:514;
B:510;
B:513;
A:505;
A:509;
B:505;
B:516;
B:509;
A:508;
B:503;
B:511;
B:507;
A:510;
B:504;
A:511;
A:507;
B:515;
A:504;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
n/a X *
AKG B:502;
A:502;
Valid;
Valid;
none;
none;
ic50 = 9 uM
146.098 C5 H6 O5 C(CC(...
MN B:501;
A:501;
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
4OCT 2.28 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN ALKBH5 CRYSTALLIZED IN THE PRESEN MN^{2+} AND 2-OXOGLUTARATE HOMO SAPIENS STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC RNDEMETHYLASE OXIDOREDUCTASE
Ref.: STRUCTURES OF HUMAN ALKBH5 DEMETHYLASE REVEAL A UNI BINDING MODE FOR SPECIFIC SINGLE-STRANDED N6-METHYL RNA DEMETHYLATION. J.BIOL.CHEM. V. 289 17299 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 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)....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 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 C(CC(=O)O)....
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 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKG; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 SIN 0.526316 0.833333
3 OOG 0.5 0.947368
4 69O 0.458333 0.714286
5 2IT 0.423077 0.615385
6 SHF 0.416667 0.666667
7 3PY 0.409091 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4OCT; Ligand: AKG; Similar sites found with APoc: 318
This union binding pocket(no: 1) in the query (biounit: 4oct.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3E2M E2M None
2 2Z77 HE7 None
3 5EZU MYR None
4 1OGX EQU None
5 1VYF OLA None
6 4JH6 FCN None
7 4EKV BTN None
8 1SWG BTN None
9 2B9J ADP 0.900901
10 5I0U DCY 1
11 1QIN GIP 1.0929
12 5C3R HMU 1.35135
13 5C3R AKG 1.35135
14 2FLI DX5 1.36364
15 4JZR 4JR 1.38889
16 3RWP ABQ 1.60772
17 6D6L FY4 1.76471
18 3OPT AKG 1.8018
19 5FQK 6NT 1.8018
20 5TFZ 7BC 2
21 1NWW HPN 2.01342
22 6FOF LAT 2.04082
23 2YGO PCF 2.12766
24 3QP8 HL0 2.17391
25 3PUA OGA 2.25225
26 6MPT C30 2.25225
27 1ODM ASV 2.25225
28 4URL XAM 2.25225
29 3WW2 SF6 2.25225
30 1GQG DCD 2.25225
31 2Y3S TIR 2.25225
32 5W4W 9WG 2.25225
33 4JGP PYR 2.30415
34 4IPH 1FJ 2.43902
35 3SCH TB6 2.52525
36 5ML3 DL3 2.68456
37 6FXR AKG 2.7027
38 5C5T AKG 2.7027
39 3N9P OGA 2.7027
40 3N9Q OGA 2.7027
41 3PG7 PTY 2.7027
42 2XK9 XK9 2.7027
43 3PUR 2HG 2.7027
44 5EW9 5VC 2.7027
45 3N9O OGA 2.7027
46 5EOB 5QQ 2.7027
47 1ZOA 140 2.7027
48 2CSN CKI 2.7027
49 5N87 N66 2.7027
50 3H7J PPY 2.7027
51 4GCZ FMN 2.7027
52 4B2Z P5S 2.7027
53 2R5N R5P 2.7027
54 2R5N RP5 2.7027
55 5HV0 AKG 2.76498
56 1Y0G 8PP 3.14136
57 3TCT 3MI 3.14961
58 3WV6 GAL BGC 3.15315
59 5M0T AKG 3.15315
60 3KV5 OGA 3.15315
61 1EWF PC1 3.15315
62 5UQD AKG 3.15315
63 6FE1 V14 3.15315
64 1VA6 P2S 3.15315
65 4GJ3 0XP 3.15315
66 3M3R BCD 3.15315
67 1QD1 FON 3.15315
68 2WKQ FMN 3.15315
69 2OVD DAO 3.2967
70 2IXC TRH 3.46535
71 2ET1 GLV 3.48259
72 2YG2 FLC 3.48837
73 2YG2 S1P 3.48837
74 6CZI 38E 3.57143
75 6D61 4AA 3.58974
76 5LUN OGA 3.6036
77 5L9V OGA 3.6036
78 5IQT 6CU 3.6036
79 4YRD 3IT 3.6036
80 5V1B 8UY 3.6036
81 2XMY CDK 3.6036
82 5DRB 5FJ 3.6036
83 5IQT AKG 3.6036
84 4IGQ THR M3L GLN 3.6036
85 1OS7 TAU 3.6036
86 1OS7 AKG 3.6036
87 3FW9 SLX 3.6036
88 5LUN ARG 3.6036
89 4IGQ OGA 3.6036
90 4QCK ASD 3.6036
91 5Y72 DST 3.6036
92 4D4U FUC GAL NAG 3.6036
93 3MF2 AMP 3.6036
94 1T27 PCW 3.6036
95 4MP8 NAD 3.6036
96 4MP8 MLI 3.6036
97 5H2D ERG 3.6036
98 2D3M COA 3.6036
99 2P7Q GG6 3.7594
100 5H9Q TD2 3.87097
101 5JSP DQY 3.9801
102 1DRY AAG 4.05405
103 1DRY AKG 4.05405
104 3OVR 5SP 4.05405
105 4YGF AZM 4.05405
106 3RGA LSB 4.05405
107 3E7O 35F 4.05405
108 4MLO PAM 4.05405
109 3PFG TLO 4.05405
110 3PFG SAM 4.05405
111 4NW6 2NS 4.05405
112 3PP0 03Q 4.05405
113 3U6W KIV 4.05405
114 4L4J NAG NAG BMA MAN NAG 4.0724
115 4ZSI 4R1 4.09357
116 4ZSI GLP 4.09357
117 3E8N VRA 4.10557
118 3E8N ATP 4.10557
119 1J3R 6PG 4.21053
120 3M3E GAL A2G NPO 4.34783
121 2D6M LBT 4.40252
122 4MNS 2AX 4.40252
123 1GT4 UNA 4.40252
124 5ANU 58T 4.43038
125 1IS3 LAT 4.44444
126 1N5S ADL 4.46429
127 3FW4 CAQ 4.49438
128 1WUB OTP 4.49438
129 5XEG AKG 4.5045
130 5O9W AKG 4.5045
131 4XCB HY0 4.5045
132 4XCB AKG 4.5045
133 6F4T OGA 4.5045
134 3ACL 3F1 4.5045
135 4OMJ 2TX 4.5045
136 1OLM VTQ 4.5045
137 2XN3 ID8 4.5045
138 3ZXE PGZ 4.51128
139 4H2V AMP 4.54545
140 4HSJ 6PC 4.5977
141 1Y9Q MED 4.6875
142 4WVW SLT 4.86111
143 3P3N AKG 4.95496
144 2Y0I AKG 4.95496
145 1H2K OGA 4.95496
146 4B7E OGA 4.95496
147 1H2M OGA 4.95496
148 2XUM OGA 4.95496
149 5JWP AKG 4.95496
150 3W8X FTK 4.95496
151 5G5W R8C 4.95496
152 1Y7P RIP 4.95496
153 2WA4 069 4.95496
154 5FBN 5WF 4.95496
155 3E8T UQ8 5
156 1WW5 SGA BGC 5
157 3NV3 GAL NAG MAN 5.07246
158 4J25 OGA 5.24017
159 1I82 BGC BGC 5.29101
160 4XIZ LPP 5.29412
161 1MDC PLM 5.30303
162 4NG2 OHN 5.30973
163 5FLJ QUE 5.37634
164 2HKA C3S 5.38462
165 1OIJ AKG 5.40541
166 4NAO AKG 5.40541
167 6EOZ 58K 5.40541
168 1OIK C26 5.40541
169 1OIK AKG 5.40541
170 4M26 ZZU 5.40541
171 5IVE 6E8 5.40541
172 4M26 AKG 5.40541
173 4M26 SIN 5.40541
174 5XVG 8FX 5.40541
175 4B0T ADP 5.40541
176 2OBD 2OB 5.40541
177 1UNB AKG 5.40541
178 3AMN CBI 5.40541
179 3AMN CBK 5.40541
180 2AE2 PTO 5.40541
181 1UNB PN1 5.40541
182 6EOZ AKG 5.40541
183 1PVN MZP 5.40541
184 4XV1 904 5.40541
185 5BU3 4W9 5.43478
186 4WUJ FMN 5.44218
187 2AG4 LP3 5.4878
188 2AG4 OLA 5.4878
189 5DKK FMN 5.51724
190 3KFF ZBT 5.55556
191 3KFF XBT 5.55556
192 1QY1 PRZ 5.74713
193 1Y2F WAI 5.7554
194 1YKD CMP 5.77889
195 2FCU AKG 5.85586
196 2OG7 SIN 5.85586
197 5NCJ SIN 5.85586
198 5NCJ HL5 5.85586
199 5LXB 7A9 5.85586
200 2RDQ AKG 5.85586
201 5ENQ 5QE 5.85586
202 2VFT SOR 5.85586
203 2AXR ABL 5.85586
204 3AGC RCC 5.85586
205 3QUZ QUV 6.06061
206 3RUG DB6 6.06061
207 2NNQ T4B 6.10687
208 1R5L VIV 6.10687
209 3SAO NKN 6.25
210 5AYT L6Y 6.28931
211 4BG1 OGA 6.30631
212 4BG1 IVL 6.30631
213 5FXD H7Y 6.30631
214 5C03 AGS 6.30631
215 5HWO HMG 6.30631
216 5YBN AKG 6.30631
217 3E85 BSU 6.32911
218 4RYV ZEA 6.45161
219 4AZP A9M 6.52174
220 5SVV FMN 6.56934
221 3DLG GWE 6.59091
222 1GP6 DH2 6.75676
223 1GP6 SIN 6.75676
224 1GP6 QUE 6.75676
225 3NNF AKG 6.75676
226 4OJ8 2TQ 6.75676
227 4BVA T3 6.75676
228 2A1L PCW 6.75676
229 3Q8G PEE 6.75676
230 4OJ8 AKG 6.75676
231 4QYN RTL 6.76692
232 5IXH OTP 6.8323
233 4R38 RBF 7.14286
234 5AIG VPR 7.2
235 4J7Q B7N 7.20721
236 3W68 VIV 7.20721
237 1JPA ANP 7.20721
238 2F9W PAU 7.20721
239 1C1L GAL BGC 7.29927
240 2GJ5 VD3 7.40741
241 5HZ5 65X 7.46269
242 2E56 MYR 7.63889
243 2YBP 2HG 7.65766
244 5F3I 5UJ 7.65766
245 2OS2 OGA 7.65766
246 3HX3 RET 7.65766
247 1E8G FCR 7.65766
248 3LKJ LKJ 7.80142
249 5NFB 8VT 7.95455
250 5FPX GLY SER SER HIS HIS HIS HIS HIS 7.9646
251 4ZXA H8N 8.10811
252 4J36 1HR 8.10811
253 4J36 FAD 8.10811
254 4F7E 0SH 8.16327
255 5KEW 6SB 8.51064
256 2XCG XCG 8.55856
257 1ULE GLA GAL NAG 8.66667
258 3D72 FAD 8.72483
259 6GNO XDI 8.88889
260 2A1X AKG 9.00901
261 4ZU5 THM 9.02778
262 2GC0 PAN 9.04255
263 4Y24 TD2 9.09091
264 4QM9 CYS 9.24856
265 4XAC AKG 9.45946
266 4WW7 AMP 9.45946
267 3GJB AKG 9.45946
268 1A78 TDG 9.70149
269 3KV4 OGA 9.90991
270 1W3T 3GR 9.90991
271 5GLT BGC GAL NAG GAL 9.90991
272 4N7C AEF 10.2273
273 2QL9 CIT 10.3093
274 4CCK OGA 10.3604
275 4CCN OGA 10.3604
276 4Y3O OGA 10.3604
277 1GZW GAL BGC 10.4478
278 1ZZ7 S0H 10.6061
279 4YZC STU 10.8108
280 3VQ2 LP4 LP5 MYR DAO 10.8108
281 1REQ DCA 11.2613
282 5FU3 BGC BGC BGC 11.3208
283 3STK PLM 11.3636
284 3QRC SCR 11.465
285 1DZK PRZ 11.465
286 3W21 AKG 11.7117
287 1NX4 AKG 11.7117
288 5KWY C3S 11.7117
289 5IXG OTP 11.8343
290 5EPA AKG 12.1622
291 3VV1 GAL FUC 12.5
292 2XXP DSL 12.6126
293 4G31 0WH 13.0631
294 5EFW FMN 13.3333
295 5DEY 59T 13.5135
296 2PR5 FMN 13.6364
297 1NYW DAU 13.7056
298 3MTX PGT 13.9073
299 3PQB VGP 13.964
300 3T50 FMN 14.0625
301 3HUJ AGH 14.1414
302 2JIG PD2 14.4144
303 2WBP ZZU 14.4144
304 2WBP SIN 14.4144
305 1S4M LUM 14.4144
306 5I8T LAC 15.0838
307 5L9B AKG 15.3153
308 3HXU A5A 16.6667
309 4XF6 LIP 16.6667
310 4XF6 INS 16.6667
311 4XF6 ADP 16.6667
312 3N0Y APC 16.7598
313 3A6T 8OG 17.0543
314 5TBM 79A 18.8034
315 1P0Z FLC 19.084
316 4C2V YJA 20.4545
317 4CCO OGA 25
318 4QXB OGA 35.2941
Pocket No.: 2; Query (leader) PDB : 4OCT; Ligand: AKG; Similar sites found with APoc: 37
This union binding pocket(no: 2) in the query (biounit: 4oct.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1TT8 PHB None
2 3VHH VHH None
3 4GGZ BTN None
4 4H6Q TFB 1.35135
5 3WW2 LPK 2.25225
6 1AUA BOG 2.7027
7 5DJU FMN 2.75862
8 3STD MQ0 3.0303
9 5HZX 2GE 3.40909
10 4D4U FUC NDG GAL FUC 3.6036
11 4D52 GIV 3.6036
12 2G50 PYR 3.6036
13 5EO8 TFU 4.05405
14 2YAK OSV 4.05405
15 5T46 MGP 4.09091
16 2JLD AG1 4.5045
17 2WMC MGP 5.05618
18 3BXO UPP 5.40541
19 1I06 TZL 5.55556
20 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 6.06061
21 4QDF 30Q 6.30631
22 1WBI BTN 6.97674
23 2Y6Q I7T 7.20721
24 6BXI ANP 7.20721
25 4K55 H6P 7.25806
26 1E8G FAD 7.65766
27 3IS2 FAD 8.44156
28 4QWT ACD 8.55856
29 4K3H 1OM 9.32203
30 5ABX MGP 9.47368
31 4QAC KK3 9.67742
32 3HAV ATP 9.90991
33 2V0U FMN 11.6438
34 2YMZ LAT 12.3077
35 6E08 NAP 13.0631
36 4RF7 ARG 13.964
37 4WO4 JLS 14
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