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 n/a X n/a
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 26 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 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 : 4OCT; Ligand: AKG; Similar sites found: 214
This union binding pocket(no: 1) in the query (biounit: 4oct.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4JH6 FCN 0.004596 0.42179 None
2 1OGX EQU 0.004866 0.42067 None
3 1VYF OLA 0.01365 0.41203 None
4 4EKV BTN 0.0107 0.4022 None
5 5I0U DCY 0.00007207 0.50116 1
6 5C3R AKG 0.00001032 0.49251 1.35135
7 5C3R HMU 0.00001032 0.49251 1.35135
8 2FLI DX5 0.00693 0.42322 1.36364
9 4JZR 4JR 0.0002481 0.48251 1.38889
10 3QCQ 3Q0 0.03316 0.43354 1.60256
11 3IX8 TX3 0.01422 0.41264 1.7341
12 3OPT AKG 0.003611 0.43309 1.8018
13 5TFZ 7BC 0.0006007 0.45225 2
14 3QP8 HL0 0.006005 0.42061 2.17391
15 1ODM ASV 0.00005515 0.53193 2.25225
16 3PUA OGA 0.0005105 0.4763 2.25225
17 4DE9 VTP 0.00121 0.47348 2.25225
18 1GQG DCD 0.01336 0.40927 2.25225
19 4IPH 1FJ 0.01897 0.40641 2.43902
20 3SCH TB6 0.0002435 0.43924 2.52525
21 5ML3 DL3 0.0009493 0.48677 2.68456
22 5C5T AKG 0.0000001655 0.6345 2.7027
23 3PUR 2HG 0.000383 0.48411 2.7027
24 2XK9 XK9 0.004476 0.4498 2.7027
25 3N9P OGA 0.000169 0.44153 2.7027
26 3N9Q OGA 0.0002311 0.43694 2.7027
27 3N9O OGA 0.0002434 0.43627 2.7027
28 5EOB 5QQ 0.02124 0.42909 2.7027
29 1ZOA 140 0.0135 0.42628 2.7027
30 2CSN CKI 0.01205 0.41768 2.7027
31 5N87 N66 0.02452 0.41182 2.7027
32 3H7J PPY 0.003108 0.4118 2.7027
33 4GCZ FMN 0.01258 0.40704 2.7027
34 4B2Z P5S 0.0369 0.40556 2.7027
35 2R5N RP5 0.03547 0.4035 2.7027
36 2R5N R5P 0.03504 0.40273 2.7027
37 5HV0 AKG 0.000000417 0.61304 2.76498
38 1Y0G 8PP 0.01175 0.43537 3.14136
39 5M0T AKG 0.0008028 0.46889 3.15315
40 3KV5 OGA 0.001234 0.46281 3.15315
41 5UQD AKG 0.0003852 0.42804 3.15315
42 3M3R BCD 0.02173 0.41857 3.15315
43 2OVD DAO 0.0007932 0.46823 3.2967
44 2IXC TRH 0.01876 0.40203 3.46535
45 2ET1 GLV 0.00001884 0.49502 3.48259
46 2YG2 FLC 0.005405 0.43503 3.48837
47 2YG2 S1P 0.00614 0.42751 3.48837
48 5L9V OGA 0.000002254 0.57129 3.6036
49 5LUN ARG 0.00001015 0.57037 3.6036
50 5LUN OGA 0.0000007991 0.56998 3.6036
51 4YRD 3IT 0.00007744 0.51722 3.6036
52 5V1B 8UY 0.00009077 0.48203 3.6036
53 2XMY CDK 0.004185 0.4736 3.6036
54 5DRB 5FJ 0.003021 0.4682 3.6036
55 5IQT AKG 0.00005043 0.45235 3.6036
56 4IGQ THR M3L GLN 0.001832 0.44746 3.6036
57 1OS7 TAU 0.00006842 0.44626 3.6036
58 1OS7 AKG 0.00006842 0.44626 3.6036
59 3FW9 SLX 0.002282 0.44286 3.6036
60 4IGQ OGA 0.00004714 0.43566 3.6036
61 4QCK ASD 0.002377 0.43541 3.6036
62 5IQT 6CU 0.00009687 0.42248 3.6036
63 3MF2 AMP 0.01133 0.41444 3.6036
64 1T27 PCW 0.03759 0.40872 3.6036
65 4MP8 NAD 0.03508 0.40671 3.6036
66 5H2D ERG 0.01864 0.40378 3.6036
67 1EPB REA 0.002423 0.40816 3.65854
68 5JSP DQY 0.003848 0.40602 3.9801
69 1DRY AAG 0.001161 0.46984 4.05405
70 1DRY AKG 0.001161 0.46984 4.05405
71 3OVR 5SP 0.002939 0.44321 4.05405
72 4WHZ 3NL 0.01469 0.43376 4.05405
73 4MLO PAM 0.007261 0.41243 4.05405
74 3SXF BK5 0.02412 0.41112 4.05405
75 3E7O 35F 0.02563 0.40753 4.05405
76 4ZSI 4R1 0.001601 0.4459 4.09357
77 4ZSI GLP 0.008265 0.4119 4.09357
78 1J3R 6PG 0.001942 0.43447 4.21053
79 4MNS 2AX 0.001431 0.48815 4.40252
80 1GT4 UNA 0.001051 0.4546 4.40252
81 2D6M LBT 0.00002092 0.42516 4.40252
82 4N1T 2GD 0.02256 0.41151 4.40252
83 1IS3 LAT 0.0003855 0.41502 4.44444
84 1N5S ADL 0.0006778 0.46368 4.46429
85 3FW4 CAQ 0.00443 0.43777 4.49438
86 1WUB OTP 0.01938 0.42395 4.49438
87 4XCB HY0 0.00001529 0.56155 4.5045
88 4XCB AKG 0.000003582 0.5415 4.5045
89 4GJY OGA 0.0004333 0.47542 4.5045
90 4NM5 ADP 0.003784 0.43783 4.5045
91 3ACL 3F1 0.005287 0.42117 4.5045
92 4OMJ 2TX 0.01487 0.42078 4.5045
93 1OLM VTQ 0.02382 0.40421 4.5045
94 4XBT 3ZQ 0.001235 0.45356 4.51613
95 4XBT FLC 0.001291 0.45263 4.51613
96 4HIA FMN 0.0135 0.4252 4.54545
97 4H2V AMP 0.0117 0.4121 4.54545
98 1Y9Q MED 0.01146 0.4068 4.6875
99 1H2K OGA 0.0005379 0.4703 4.95496
100 1H2M OGA 0.0006479 0.46608 4.95496
101 3P3N AKG 0.0008109 0.46167 4.95496
102 4B7E OGA 0.001039 0.45973 4.95496
103 2Y0I AKG 0.002031 0.44488 4.95496
104 2WA4 069 0.001066 0.43966 4.95496
105 2XUM OGA 0.0007001 0.42565 4.95496
106 5G5W R8C 0.01479 0.41463 4.95496
107 5FBN 5WF 0.03636 0.4019 4.95496
108 3E8T UQ8 0.03333 0.41991 5
109 4J25 OGA 0.0000007973 0.55474 5.24017
110 4XIZ LPP 0.03667 0.40064 5.29412
111 1MDC PLM 0.003954 0.43689 5.30303
112 4NG2 OHN 0.01799 0.40756 5.30973
113 1OIK C26 0.0001493 0.49495 5.40541
114 1OIK AKG 0.000007624 0.49466 5.40541
115 1OIJ AKG 0.000004745 0.48506 5.40541
116 4M26 SIN 0.0006449 0.4809 5.40541
117 4M26 AKG 0.0006935 0.46938 5.40541
118 5IVE 6E8 0.001752 0.46537 5.40541
119 4NAO AKG 0.0000446 0.45283 5.40541
120 4B0T ADP 0.006547 0.42937 5.40541
121 1UNB AKG 0.00001312 0.42691 5.40541
122 2X4Z X4Z 0.0143 0.42279 5.40541
123 3AMN CBI 0.01086 0.41694 5.40541
124 3AMN CBK 0.01086 0.41694 5.40541
125 1UNB PN1 0.00001555 0.41423 5.40541
126 4XV1 904 0.03394 0.40237 5.40541
127 5BU3 4W9 0.00426 0.43354 5.43478
128 5DKK FMN 0.01205 0.40795 5.51724
129 3KFF XBT 0.0003357 0.4532 5.55556
130 3KFF ZBT 0.0003357 0.4532 5.55556
131 1QY1 PRZ 0.0002961 0.48998 5.74713
132 2FCU AKG 0.000001229 0.54665 5.85586
133 2RDQ AKG 0.0007163 0.47129 5.85586
134 2OG7 SIN 0.00005077 0.45211 5.85586
135 5ENQ 5QE 0.01507 0.41139 5.85586
136 2VFT SOR 0.008444 0.40465 5.85586
137 2AXR ABL 0.01484 0.40355 5.85586
138 3AGC RCC 0.02639 0.40196 5.85586
139 2NNQ T4B 0.00689 0.4435 6.10687
140 1R5L VIV 0.003885 0.44059 6.10687
141 3SAO NKN 0.01091 0.40403 6.25
142 4BG1 IVL 0.001481 0.45592 6.30631
143 4Q0L V14 0.007716 0.42583 6.30631
144 5FXD H7Y 0.006587 0.41661 6.30631
145 5C03 AGS 0.01376 0.40327 6.30631
146 4AZP A9M 0.01214 0.41455 6.52174
147 1GP6 SIN 0.000001799 0.60536 6.75676
148 1GP6 DH2 0.000001799 0.60536 6.75676
149 1GP6 QUE 0.000002001 0.60536 6.75676
150 3NNF AKG 0.000001734 0.52355 6.75676
151 4BVA T3 0.003229 0.46162 6.75676
152 2A1L PCW 0.004413 0.45861 6.75676
153 3Q8G PEE 0.01063 0.446 6.75676
154 4OJ8 AKG 0.001639 0.40243 6.75676
155 4QYN RTL 0.01631 0.40664 6.76692
156 5IXH OTP 0.01244 0.43407 6.8323
157 4R38 RBF 0.007249 0.42049 7.14286
158 5AIG VPR 0.002927 0.42615 7.2
159 3W68 VIV 0.002127 0.45009 7.20721
160 4J7Q B7N 0.00557 0.44493 7.20721
161 2F9W PAU 0.005095 0.41964 7.20721
162 1C1L GAL BGC 0.0003076 0.49406 7.29927
163 2GJ5 VD3 0.003285 0.45901 7.40741
164 2E56 MYR 0.0143 0.41926 7.63889
165 5F3I 5UJ 0.008168 0.45213 7.65766
166 2YBP 2HG 0.0007892 0.42949 7.65766
167 2OS2 OGA 0.001055 0.42549 7.65766
168 3HX3 RET 0.00739 0.41628 7.65766
169 3LKJ LKJ 0.02242 0.4105 7.80142
170 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.0006459 0.41804 7.9646
171 4ZXA H8N 0.0003698 0.47421 8.10811
172 5BVE 4VG 0.0368 0.42018 8.10811
173 5KEW 6SB 0.002256 0.42389 8.51064
174 1ULE GLA GAL NAG 0.01377 0.40595 8.66667
175 2A1X AKG 0.00009314 0.42742 9.00901
176 5BYZ 4WE 0.01574 0.41714 9.00901
177 2GC0 PAN 0.001715 0.40719 9.04255
178 4Y24 TD2 0.003048 0.42533 9.09091
179 1SN0 T44 0.01025 0.40309 9.23077
180 4QM9 CYS 0.0003014 0.43359 9.24856
181 4XAC AKG 0.00001234 0.50756 9.45946
182 4WW7 AMP 0.01279 0.41019 9.45946
183 3KV4 OGA 0.001141 0.46001 9.90991
184 4CCN OGA 0.0001901 0.4963 10.3604
185 4Y3O OGA 0.0002777 0.43825 10.3604
186 4CCK OGA 0.0002991 0.437 10.3604
187 1GZW GAL BGC 0.007403 0.41771 10.4478
188 1ZZ7 S0H 0.003591 0.41014 10.6061
189 4YZC STU 0.003224 0.45943 10.8108
190 3VQ2 LP4 LP5 MYR DAO 0.004913 0.4552 10.8108
191 4QJP V1F 0.009523 0.4213 10.8108
192 1REQ DCA 0.02556 0.41847 11.2613
193 5FU3 BGC BGC BGC 0.003864 0.40048 11.3208
194 3QRC SCR 0.00002851 0.52285 11.465
195 1DZK PRZ 0.001491 0.41529 11.465
196 1NX4 AKG 0.000487 0.43608 11.7117
197 3W21 AKG 0.0001612 0.43549 11.7117
198 5IXG OTP 0.01701 0.42954 11.8343
199 5EPA AKG 0.00004184 0.49642 12.1622
200 5DEY 59T 0.00954 0.44697 13.5135
201 1NYW DAU 0.01447 0.40409 13.7056
202 3MTX PGT 0.003123 0.45403 13.9073
203 3PQB VGP 0.003074 0.44046 13.964
204 3HUJ AGH 0.03562 0.41477 14.1414
205 2JIG PD2 0.000001657 0.56645 14.4144
206 2WBP ZZU 0.0006217 0.40532 14.4144
207 2WBP SIN 0.0006217 0.40532 14.4144
208 1S4M LUM 0.02179 0.40481 14.4144
209 5L9B AKG 0.000003489 0.56245 15.3153
210 1RYA GDP 0.02676 0.40033 16.25
211 3A6T 8OG 0.002041 0.41211 17.0543
212 4C2V YJA 0.02097 0.40957 20.4545
213 4CCO OGA 0.001407 0.45223 25
214 4QXB OGA 0.0001677 0.47559 35.2941
Pocket No.: 2; Query (leader) PDB : 4OCT; Ligand: AKG; Similar sites found: 22
This union binding pocket(no: 2) in the query (biounit: 4oct.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4GGZ BTN 0.007379 0.40739 None
2 1AUA BOG 0.01575 0.40047 2.7027
3 5HZX 2GE 0.004833 0.41598 3.40909
4 1IF7 SBR 0.04455 0.42849 3.6036
5 3S7O LBV 0.03475 0.40073 3.6036
6 2YAK OSV 0.02744 0.40364 4.05405
7 5T46 MGP 0.01816 0.40527 4.09091
8 3W8X FTK 0.01191 0.4 4.95496
9 2WMC MGP 0.01408 0.4134 5.05618
10 2HKA C3S 0.001235 0.40384 5.38462
11 4WUJ FMN 0.01714 0.40052 5.44218
12 1YKD CMP 0.01466 0.40195 5.77889
13 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 0.02298 0.40995 6.06061
14 4QDF 30Q 0.01329 0.40204 6.30631
15 1WBI BTN 0.01307 0.4003 6.97674
16 2Y6Q I7T 0.03975 0.41145 7.20721
17 3IS2 FAD 0.0306 0.4 8.44156
18 4QWT ACD 0.02305 0.40359 8.55856
19 4K3H 1OM 0.01324 0.40776 9.32203
20 4PSB GA3 0.03354 0.40371 10.3226
21 5D48 L96 0.02564 0.40126 15.7895
22 4XT2 43L 0.01635 0.40659 18.1818
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