Receptor
PDB id Resolution Class Description Source Keywords
2WL9 1.9 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF CATECHOL 2,3-DIOXYGENASE RHODOCOCCUS SP. DK17 AROMATIC HYDROCARBONS CATABOLISM IRON OXIDOREDUCTASE
Ref.: SUBSTRATE-BINDING MECHANISM OF A TYPE I EXTRADIOL DIOXYGENASE. J.BIOL.CHEM. V. 285 34643 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:1301;
B:1300;
C:1300;
D:1301;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
55.845 Fe [Fe+3...
GOL A:1303;
A:1304;
D:1302;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MBD B:1301;
D:1303;
Valid;
Valid;
none;
none;
submit data
124.137 C7 H8 O2 Cc1cc...
MG A:1302;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2WL9 1.9 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF CATECHOL 2,3-DIOXYGENASE RHODOCOCCUS SP. DK17 AROMATIC HYDROCARBONS CATABOLISM IRON OXIDOREDUCTASE
Ref.: SUBSTRATE-BINDING MECHANISM OF A TYPE I EXTRADIOL DIOXYGENASE. J.BIOL.CHEM. V. 285 34643 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 2WL9 - MBD C7 H8 O2 Cc1cccc(c1....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 2WL9 - MBD C7 H8 O2 Cc1cccc(c1....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 177 families.
1 1KND - TBU C4 H10 O CC(C)(C)O
2 1KMY Kd = 8 uM BPY C12 H10 O2 c1ccc(cc1)....
3 1LKD - BP6 C12 H8 Cl2 O2 c1cc(c(c(c....
4 1HAN - TBU C4 H10 O CC(C)(C)O
5 2WL9 - MBD C7 H8 O2 Cc1cccc(c1....
6 1KW6 - BPY C12 H10 O2 c1ccc(cc1)....
7 1KW8 - BPY C12 H10 O2 c1ccc(cc1)....
8 1EIR - BPY C12 H10 O2 c1ccc(cc1)....
9 1KWC - BPY C12 H10 O2 c1ccc(cc1)....
10 1KW9 - BPY C12 H10 O2 c1ccc(cc1)....
11 2ZI8 - SDT C19 H24 O4 Cc1ccc(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MBD; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 MBD 1 1
2 2MY 0.583333 0.736842
3 PYG 0.5 0.809524
4 JZ0 0.444444 0.777778
5 3CE 0.4 0.772727
6 3FA 0.4 0.772727
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2WL9; Ligand: MBD; Similar sites found: 252
This union binding pocket(no: 1) in the query (biounit: 2wl9.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ZZS TRP 0.0001462 0.4401 None
2 1QJC PNS 0.0006428 0.4366 None
3 3UEC ALA ARG TPO LYS 0.01828 0.41341 None
4 4HE2 AMP 0.0006227 0.41422 1.31148
5 2PN6 GLN 0.002054 0.43027 1.33333
6 4LCQ URQ 0.000002584 0.48609 1.63934
7 3M0J OAF 0.00004006 0.45211 1.63934
8 4OYA 1VE 0.001727 0.44522 1.63934
9 1RM4 NDP 0.002328 0.42149 1.63934
10 2GJ3 FAD 0.0003823 0.42021 1.66667
11 2NLI FMN 0.00002299 0.48405 1.96721
12 2NLI LAC 0.00002299 0.48405 1.96721
13 1PEA ACM 0.00191 0.4677 1.96721
14 4MWV BCZ 0.0001137 0.44637 1.96721
15 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.000404 0.4408 1.96721
16 2F2U M77 0.004089 0.41611 1.96721
17 3V91 UPG 0.00003736 0.47464 2.06186
18 2ZO9 MLI 0.001342 0.43289 2.18978
19 3MMR ABH 0.00003031 0.48406 2.29508
20 1SAY PYR 0.0002896 0.48191 2.29508
21 1DXY NAD 0.0003092 0.47012 2.29508
22 4HZX G39 0.00003275 0.46684 2.29508
23 3AIQ HBO 0.0002393 0.44398 2.29508
24 3MAG 3MA 0.01304 0.44122 2.29508
25 1FA2 DOM 0.0001901 0.42744 2.29508
26 2MAS PIR 0.008836 0.42313 2.29508
27 4KQL 1SG 0.009673 0.40098 2.29508
28 1WVC CTP 0.01329 0.40617 2.3166
29 2X61 CH 0.0001476 0.4452 2.32558
30 2P2V CSF 0.0000378 0.47664 2.43056
31 2BNF UTP 0.001438 0.41138 2.48963
32 1I9G SAM 0.0002298 0.44564 2.5
33 1OD6 PNS 0.006739 0.40003 2.5
34 1DQX BMP 0.01733 0.41446 2.62172
35 2RDT 2RD 0.000001721 0.53777 2.62295
36 1K97 ASP 0.00005237 0.49369 2.62295
37 1K97 CIR 0.00005237 0.49369 2.62295
38 4A8T PAO 0.00008259 0.47431 2.62295
39 2RDT FMN 0.0001779 0.45731 2.62295
40 4A8H PUW 0.00005273 0.44749 2.62295
41 4G87 UD1 0.0003796 0.43877 2.62295
42 1RZM PEP 0.002423 0.43584 2.62295
43 1RZM E4P 0.006914 0.43348 2.62295
44 4E28 0MZ 0.004591 0.4295 2.62295
45 2YYJ FAD 0.005173 0.4203 2.62295
46 2YYJ 4HP 0.005173 0.4203 2.62295
47 4CCN OGA 0.004684 0.41941 2.62295
48 1SQ5 PAU 0.006101 0.41873 2.62295
49 1XMV ADP 0.002451 0.41521 2.62295
50 3PLN U5P 0.007852 0.41405 2.62295
51 1ML4 PAL 0.0001424 0.41353 2.62295
52 1R6D NAD 0.004273 0.40846 2.62295
53 4Q3S X7A 0.0002827 0.40423 2.62295
54 4Q3R XA2 0.0008038 0.40297 2.62295
55 4IAE 1DX 0.001107 0.42579 2.6455
56 3K9W 4PS 0.004086 0.42968 2.6738
57 3K9W ADE 0.004086 0.42968 2.6738
58 2FWP CIT 0.00003147 0.45544 2.73224
59 2FWP ICR 0.001964 0.40345 2.73224
60 1R0X ATP 0.0007931 0.41365 2.7972
61 1DRV A3D 0.0000148 0.48837 2.9304
62 4N02 FNR 0.000007414 0.50319 2.95082
63 1N6B DMZ 0.00002201 0.46975 2.95082
64 1I2B USQ 0.0008553 0.46502 2.95082
65 1I2B NAD 0.0008553 0.46502 2.95082
66 1I2B UPG 0.0008553 0.46502 2.95082
67 3K37 BCZ 0.0009786 0.44449 2.95082
68 2YP9 SIA CMO 0.0004574 0.43567 2.95082
69 3CKZ ZMR 0.0004702 0.43085 2.95082
70 1XP8 AGS 0.00107 0.42202 2.95082
71 3DGB MUC 0.002656 0.41884 2.95082
72 3MKN DNB 0.01334 0.41324 2.95082
73 1O6B ADP 0.0005184 0.43265 2.95858
74 1P0Z FLC 0.009778 0.40434 3.05344
75 3C2O NTM 0.01717 0.40483 3.06122
76 2DUA OXL 0.00004567 0.42392 3.10345
77 2A0W DIH 0.0001799 0.43507 3.11419
78 3IU9 T07 0.006954 0.40402 3.125
79 4DA6 GA2 0.0005729 0.43963 3.16206
80 4HZD COA 0.002397 0.40064 3.19149
81 4LWM MHO 0.0224 0.45238 3.22581
82 4KS1 2H8 0.000002937 0.50715 3.27869
83 1ME8 RVP 0.00003522 0.4986 3.27869
84 2QS8 MET 0.000007095 0.47231 3.27869
85 3CL7 HYN 0.00002165 0.44928 3.27869
86 1A5Z NAD 0.0004155 0.43893 3.27869
87 4CMF PXG 0.0007082 0.4329 3.27869
88 1WDA BAG 0.004301 0.42006 3.27869
89 1JQ5 NAD 0.0137 0.41958 3.27869
90 3O9P MHI 0.004174 0.41597 3.27869
91 2PYW ADP 0.02005 0.40858 3.27869
92 5A2J ALA PRO ASP THR ARG PRO 0.03643 0.40738 3.27869
93 1A5Z FBP 0.0001735 0.40374 3.27869
94 4TMK T5A 0.00008108 0.50026 3.28639
95 1YRX FMN 0.001662 0.42202 3.30579
96 1FNZ A2G 0.001079 0.40425 3.37553
97 2RHW C0E 0.00002025 0.49593 3.53357
98 4QCK ASD 0.00001262 0.45856 3.60656
99 2VJJ RAM GLC GAL NAG NAG GLC 0.006989 0.44979 3.60656
100 3ZGJ RMN 0.00205 0.44202 3.60656
101 4QN7 G39 0.0002773 0.43107 3.60656
102 1ONX ASP 0.00006822 0.42392 3.60656
103 2BLE 5GP 0.003725 0.41429 3.60656
104 3UXL CFI 0.04822 0.40903 3.60656
105 1JAK IFG 0.01715 0.4037 3.60656
106 1NVU GTP 0.0001442 0.46049 3.61446
107 1NVV GNP 0.0001656 0.45839 3.61446
108 3L8W XAN 0.003442 0.41403 3.71622
109 4GQB 0XU 0.00003413 0.48026 3.93443
110 4TSK NDP 0.00008614 0.47013 3.93443
111 1TFZ 869 0.007688 0.43029 3.93443
112 1HV9 UD1 0.0005267 0.41797 3.93443
113 1FWY UD1 0.0005913 0.41636 3.93443
114 1HV9 COA 0.003506 0.40731 3.93443
115 1WL4 COA 0.004077 0.40146 3.93443
116 4AAW R84 0.005378 0.40095 3.93443
117 3Q3C NAD 0.0003918 0.44359 4.01338
118 3O03 NAP 0.001704 0.42473 4.12371
119 3NJQ NJQ 0.0003872 0.41447 4.14508
120 4I9A NCN 0.0008589 0.40686 4.16667
121 3KMT SAH 0.003352 0.41052 4.20168
122 1X1T NAD 0.002809 0.42535 4.23077
123 2R7K ACP 0.0001243 0.48666 4.2623
124 2R7K AMZ 0.0001243 0.48666 4.2623
125 1P4C FMN 0.0001304 0.47051 4.2623
126 3HPF GAE 0.00004619 0.45635 4.2623
127 4N4J HG1 0.001794 0.40986 4.2623
128 1PJ6 FOL 0.002727 0.40734 4.2623
129 3ZZL TRP 0.002571 0.40414 4.28571
130 4NVP 7CH 0.00015 0.43974 4.30622
131 3F81 STT 0.04238 0.40119 4.37158
132 1C1L GAL BGC 0.02004 0.41151 4.37956
133 1ZK4 NAP 0.00002584 0.50352 4.38247
134 1ZK4 AC0 0.00002584 0.50352 4.38247
135 4EKV BTN 0.00009712 0.44296 4.40252
136 4COQ SAN 0.01423 0.41297 4.45344
137 3KDJ A8S 0.01736 0.40936 4.45545
138 1SS4 CIT 0.009985 0.49409 4.57516
139 1SS4 GSH 0.009223 0.46338 4.57516
140 1AL8 FMN 0.000004142 0.50963 4.59016
141 1GSA ADP 0.000004898 0.50475 4.59016
142 1AL8 DHP 0.00009572 0.47371 4.59016
143 1GSA GSH 0.0002613 0.43936 4.59016
144 1LDM NAD 0.001106 0.43587 4.59016
145 1D3V ABH 0.0003344 0.41471 4.59016
146 3P3N AKG 0.01567 0.41104 4.59016
147 3DCT 064 0.01832 0.41711 4.68085
148 3SHR CMP 0.007845 0.40476 4.68227
149 3MB5 SAM 0.000007655 0.50047 4.70588
150 2XD9 XD9 0.001007 0.46625 4.79042
151 1G6O ADP 0.001188 0.42861 4.84848
152 3OIG IMJ 0.0003337 0.42573 4.88722
153 3OIG NAD 0.002444 0.42075 4.88722
154 3QVL 5HY 0.0003415 0.44473 4.89796
155 3RO7 TDR 0.00008066 0.49372 4.90566
156 1YBH FAD 0.0001272 0.48209 4.91803
157 1G41 ADP 0.0001248 0.46267 4.91803
158 3ZPG 5GP 0.02567 0.41834 4.91803
159 4HPP GLU 0.0007661 0.41674 4.91803
160 2NZ2 CIR 0.0003953 0.41419 4.91803
161 2AEB ABH 0.000984 0.41129 4.91803
162 3S9K CIT 0.02499 0.43418 5.08475
163 1OMZ UD2 0.0001096 0.45429 5.11945
164 1GR0 NAD 0.0001498 0.47281 5.2459
165 3SUC ATP 0.0001264 0.44617 5.2459
166 2NSX IFM 0.004059 0.43504 5.2459
167 2EAE LBT 0.009167 0.41319 5.2459
168 1Z34 2FD 0.0004739 0.43983 5.53191
169 2QLX RM4 0.002819 0.45192 5.55556
170 4FR3 0V4 0.001316 0.4366 5.55556
171 4FR3 LYS ARG ARG LYS SEP VAL 0.007534 0.40925 5.55556
172 4A3R CIT 0.0000289 0.46296 5.57377
173 1Y9Q MED 0.005756 0.43096 5.72917
174 2QXX TTP 0.0007728 0.41661 5.78947
175 1JH7 UVC 0.0002419 0.43688 5.82011
176 2OWZ F6P 0.00003227 0.46705 5.90164
177 2IMP NAI 0.003531 0.4253 5.90164
178 1O9U ADZ 0.02297 0.42084 5.90164
179 2IMP LAC 0.0001382 0.40541 5.90164
180 2VOT NHV 0.0174 0.40473 5.90164
181 2ET1 GLV 0.00002497 0.46936 5.97015
182 2PR5 FMN 0.001189 0.41432 6.06061
183 2GGH NLQ 0.00002616 0.46436 6.22951
184 1F8F NAD 0.0001936 0.45604 6.22951
185 2JE7 XMM 0.00009672 0.43316 6.27615
186 4IVG ANP 0.00002259 0.48432 6.55738
187 1ZFJ IMP 0.002162 0.44057 6.55738
188 1V5F FAD 0.006611 0.43607 6.55738
189 1V5F TPP 0.006611 0.43607 6.55738
190 1Z4V DAN 0.0002048 0.43255 6.55738
191 1JQN DCO 0.00006007 0.4005 6.55738
192 1RSD PSB 0.01075 0.43242 6.61157
193 1VQ2 DDN 0.0000125 0.50335 6.73575
194 4Q0P 0MK 0.0001788 0.48017 6.88525
195 3FPZ AHZ 0.0002115 0.47009 6.88525
196 2FH5 GTP 0.002491 0.40866 7.02703
197 3VGL BGC 0.000003751 0.48101 7.21311
198 3VGL ANP 0.0001074 0.44718 7.21311
199 4B7J G39 0.0001341 0.43846 7.21311
200 4HA6 FAD 0.002232 0.41027 7.21311
201 2TOH HBI 0.0007861 0.40154 7.21311
202 2W8Q SIN 0.00002082 0.43902 7.54098
203 3RF4 FUN 0.0003729 0.47046 7.75862
204 1T26 NAI 0.0009354 0.45323 7.86885
205 1T26 GBD 0.0009354 0.45323 7.86885
206 4P87 4NP 0.0007232 0.40605 7.86885
207 2PP3 LGT 0.0000111 0.40254 7.86885
208 2C1Q BTN 0.000003221 0.50015 7.93651
209 1Q3Q ANP 0.001297 0.42889 8.19672
210 1D09 PAL 0.02599 0.40295 8.49673
211 3D2M COA 0.0008938 0.45602 8.52459
212 4AF0 IMP 0.0001445 0.45459 8.52459
213 4AF0 MOA 0.00003039 0.44477 8.52459
214 2Z5Y HRM 0.00004942 0.41713 8.52459
215 4QN6 LNV 0.001844 0.40669 8.52459
216 1EXB NDP 0.0003846 0.45658 8.73786
217 1WKL ATP 0.0003032 0.44651 8.75912
218 1WKL ADP 0.0006704 0.42571 8.75912
219 4LBP 1WG 0.0008913 0.40635 9
220 2HMT NAI 0.0002623 0.44575 9.02778
221 4LTN NAI 0.001447 0.42044 9.13706
222 4LTN FMN 0.001113 0.42044 9.13706
223 1LTH NAD 0.0001624 0.45682 9.18033
224 3VC3 C6P 0.02911 0.40767 9.18033
225 3VKX T3 0.0003553 0.4001 9.1954
226 2H6B 3C4 0.0001349 0.4615 9.2
227 2BTO GTP 0.001437 0.41139 9.25926
228 4JH6 FCN 0.005273 0.40352 9.42029
229 4C0C WVH 0.002726 0.4083 9.63597
230 2P7Q GG6 0.01226 0.40524 9.77444
231 1QW9 KHP 0.0007232 0.40438 10.1639
232 2DYS PGV 0.02051 0.42653 10.1695
233 2DYR PGV 0.03478 0.41532 10.1695
234 1NKI PPF 0.003832 0.42707 10.3704
235 2R5V HHH 0.0006871 0.47445 10.8197
236 3UC5 ATP 0.00001539 0.4973 10.828
237 1K27 MTM 0.000599 0.41618 10.9541
238 4G1V FAD 0.00001738 0.51875 11.4754
239 1OFH ADP 0.0006025 0.44137 11.4943
240 1RP0 AHZ 0.002245 0.42759 11.6197
241 1UGX GAL MGC 0.00007343 0.41187 12.0301
242 4AP9 1PS 0.000221 0.40721 12.4378
243 1F7K UMP 0.0002138 0.41725 12.5
244 2IFB PLM 0.0256 0.4057 13.7405
245 1V8K ANP 0.0001794 0.43141 15.4098
246 2BJK NAD 0.002331 0.4172 16.0656
247 2P8B NSK 0.0002174 0.48235 16.7213
248 1F1V DHY 0.000004865 0.53518 18.0328
249 4F4S EFO 0.007081 0.41597 18.4211
250 3KPE TM3 0.01249 0.41556 28.2051
251 3HPY MCT 0.000009341 0.55674 42.623
252 1LGT BP3 0.0115 0.42114 48.8215
Pocket No.: 2; Query (leader) PDB : 2WL9; Ligand: MBD; Similar sites found: 45
This union binding pocket(no: 2) in the query (biounit: 2wl9.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2P4T NAP 0.0001404 0.4348 None
2 4F8L GAL 0.03778 0.42379 2.06897
3 3DU4 KAP 0.005257 0.42189 2.29508
4 2R85 AMP 0.003965 0.40416 2.29508
5 2YVF FAD 0.007759 0.40372 2.29508
6 2X61 NGA GAL SIA 0.0001906 0.45806 2.32558
7 3TA2 AKG 0.000958 0.40537 2.54237
8 1RYI FAD 0.003362 0.40233 2.62295
9 3F3E LEU 0.00263 0.40163 2.62295
10 3NGU ADP 0.00308 0.41191 2.64901
11 4GLJ RHB 0.0005743 0.41677 2.6936
12 3QV9 QV7 0.003585 0.43424 2.95082
13 1TV5 ORO 0.002808 0.40715 2.95082
14 1MVQ MMA 0.00102 0.40741 2.9661
15 2J5S KTA 0.00003056 0.42334 3.04183
16 2IYG FMN 0.001449 0.42907 3.22581
17 1YOE RIB 0.00007965 0.43931 3.27869
18 4MOB COA 0.0008037 0.4197 3.27869
19 3GE7 AFQ 0.0005286 0.41931 3.27869
20 1QF5 GDP 0.004282 0.40433 3.27869
21 1QF5 RPL 0.004282 0.40433 3.27869
22 1QCA FUA 0.0003365 0.45503 3.28639
23 1UJ2 C5P 0.02728 0.40854 3.57143
24 3GD8 GOL 0.0005729 0.40575 3.58744
25 2ZX7 ZX7 0.001026 0.40663 3.60656
26 4OAR 2S0 0.02637 0.40181 3.87597
27 1G8S MET 0.004604 0.43539 3.91304
28 1JCM 137 0.0003832 0.41787 4.2471
29 3FSJ D7K 0.003322 0.42147 4.2623
30 1RY2 AMP 0.000915 0.40123 4.2623
31 1TUV VK3 0.04586 0.40523 4.38596
32 1G7V PAI 0.001427 0.4126 4.57746
33 2Q6K ADN 0.01334 0.40138 4.59364
34 3BEJ MUF 0.01961 0.41159 4.62185
35 4DEM YS4 0.01199 0.40683 4.91803
36 1E7S NAP 0.001569 0.40281 4.91803
37 4C25 13P 0.0008942 0.40631 5.18868
38 1V7R CIT 0.0373 0.41657 5.91398
39 1EYE PMM 0.004912 0.40845 6.78571
40 2V5E SCR 0.03525 0.4179 6.93069
41 1OTH PAO 0.00122 0.4063 7.21311
42 2JEN GLC GLC BGC XYS BGC XYS 0.00902 0.40758 7.27969
43 1SJW NGV 0.0008605 0.42803 8.33333
44 2Z6C FMN 0.01428 0.41395 10.0775
45 3DJL FAD 0.005421 0.41847 17.7049
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