Receptor
PDB id Resolution Class Description Source Keywords
2V5K 2.2 Å EC: 4.1.2.- CLASS II ALDOLASE HPCH - MAGNESIUM - OXAMATE COMPLEX ESCHERICHIA COLI LYASE CLASS II ALDOLASE HOMOPROTOCATECHUATE AROMATIC DEGRAROMATIC HYDROCARBONS CATABOLISMHOMOPROTOCATECHUATE
Ref.: STRUCTURE AND MECHANISM OF HPCH: A METAL ION DEPEND CLASS II ALDOLASE FROM THE HOMOPROTOCATECHUATE DEGR PATHWAY OF ESCHERICHIA COLI. J.MOL.BIOL. V. 373 866 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:301;
B:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
OXM A:302;
B:302;
Valid;
Valid;
none;
none;
submit data
89.05 C2 H3 N O3 C(=O)...
PO4 A:1260;
B:1260;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2V5K 2.2 Å EC: 4.1.2.- CLASS II ALDOLASE HPCH - MAGNESIUM - OXAMATE COMPLEX ESCHERICHIA COLI LYASE CLASS II ALDOLASE HOMOPROTOCATECHUATE AROMATIC DEGRAROMATIC HYDROCARBONS CATABOLISMHOMOPROTOCATECHUATE
Ref.: STRUCTURE AND MECHANISM OF HPCH: A METAL ION DEPEND CLASS II ALDOLASE FROM THE HOMOPROTOCATECHUATE DEGR PATHWAY OF ESCHERICHIA COLI. J.MOL.BIOL. V. 373 866 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2V5K - OXM C2 H3 N O3 C(=O)(C(=O....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2V5K - OXM C2 H3 N O3 C(=O)(C(=O....
2 4B5V - PYR C3 H4 O3 CC(=O)C(=O....
3 4B5T - 2KT C4 H6 O3 CCC(=O)C(=....
4 4B5W Kd = 26.9 mM PYR C3 H4 O3 CC(=O)C(=O....
5 4B5S - PYR C3 H4 O3 CC(=O)C(=O....
6 4B5U - PYR C3 H4 O3 CC(=O)C(=O....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2V5K - OXM C2 H3 N O3 C(=O)(C(=O....
2 2VWT - PYR C3 H4 O3 CC(=O)C(=O....
3 4B5V - PYR C3 H4 O3 CC(=O)C(=O....
4 4B5T - 2KT C4 H6 O3 CCC(=O)C(=....
5 4B5W Kd = 26.9 mM PYR C3 H4 O3 CC(=O)C(=O....
6 4B5S - PYR C3 H4 O3 CC(=O)C(=O....
7 4B5U - PYR C3 H4 O3 CC(=O)C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: OXM; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 OXM 1 1
2 MLM 0.466667 0.607143
3 PYM 0.461538 0.636364
4 HGY 0.4 0.904762
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V5K; Ligand: OXM; Similar sites found: 290
This union binding pocket(no: 1) in the query (biounit: 2v5k.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QDT A2G GAL 0.0002951 0.48568 None
2 1UO4 PIH 0.001525 0.47115 None
3 2GJ3 FAD 0.000258 0.47038 None
4 3QDW A2G 0.001664 0.45948 None
5 1NU4 MLA 0.006682 0.448 None
6 1PTR PRB 0.003552 0.42817 None
7 3KPE TM3 0.003376 0.42247 None
8 1C3M MAN MAN 0.001002 0.42134 None
9 1ECM TSA 0.002017 0.41399 None
10 3QDY A2G GAL 0.01046 0.41358 None
11 1NPL MAN 0.0001377 0.41025 None
12 1B66 BIO 0.004713 0.40807 None
13 1WKL ATP 0.0002376 0.40529 None
14 4E03 ADP 0.01773 0.40499 None
15 4F4S EFO 0.00553 0.40205 None
16 1Y7P RIP 0.01877 0.4017 None
17 2E1A MSE 0.004581 0.40021 None
18 1BTN I3P 0.0133 0.43939 1.0453
19 1SBZ FMN 0.002779 0.43053 1.52284
20 1C9K 5GP 0.001376 0.45185 1.66667
21 3NOJ PYR 0.01484 0.40791 1.68067
22 1V1A KDG 0.00005509 0.47996 1.74216
23 2YYJ 4HP 0.002634 0.46697 1.74216
24 2YYJ FAD 0.002634 0.46697 1.74216
25 1V1A ADP 0.0003228 0.4641 1.74216
26 2CSN CKI 0.001444 0.43328 1.74216
27 2Y65 ADP 0.0115 0.40476 1.74216
28 2H29 DND 0.04144 0.4036 1.74216
29 1I9G SAM 0.002504 0.44655 1.78571
30 3R51 MMA 0.01651 0.411 1.875
31 1D09 PAL 0.006523 0.45839 1.96078
32 2HMT NAI 0.00008635 0.51115 2.08333
33 4IVG ANP 0.003936 0.44162 2.09059
34 4MWV BCZ 0.002722 0.43688 2.09059
35 1J99 AND 0.02939 0.41045 2.09059
36 4RJK PYR 0.01516 0.40605 2.09059
37 4M51 BEZ 0.01982 0.40059 2.09059
38 4LZB URA 0.03984 0.41062 2.10084
39 2NT8 ATP 0.007327 0.40951 2.24215
40 1Z42 HBA 0.002209 0.47601 2.43902
41 1Z44 NPO 0.006385 0.44906 2.43902
42 1GQG DCD 0.003743 0.44873 2.43902
43 1NJF ADP 0.004921 0.44353 2.43902
44 1NJF AGS 0.01061 0.4273 2.43902
45 2FGQ MLT 0.002981 0.42479 2.43902
46 3L6R MLI 0.004525 0.42347 2.43902
47 1G3M PCQ 0.04201 0.40858 2.43902
48 3LRE ADP 0.01033 0.40376 2.43902
49 2Q1A 2KT 0.009887 0.40237 2.43902
50 4A6F SEP 0.02199 0.41207 2.5
51 1D8C GLV 0.00001795 0.52554 2.78746
52 1LTH NAD 0.000348 0.48898 2.78746
53 4N02 FNR 0.002835 0.44944 2.78746
54 1D3V ABH 0.0005957 0.44853 2.78746
55 1OTH PAO 0.001603 0.44027 2.78746
56 2PA4 UPG 0.008316 0.43982 2.78746
57 1DKU AP2 0.004027 0.41787 2.78746
58 1LTH FBP 0.0001164 0.4164 2.78746
59 2GWD GLU 0.001819 0.41572 2.78746
60 3H22 B53 0.01325 0.40757 2.78746
61 1TIW FAD 0.01625 0.40548 2.78746
62 1TIW TFB 0.01625 0.40548 2.78746
63 1SOW NAD 0.01168 0.40502 2.78746
64 1KK1 GNP 0.01835 0.4002 2.78746
65 4COQ SAN 0.008519 0.40516 2.83401
66 4HZD COA 0.001925 0.4408 2.83688
67 1WGC SIA GAL BGC 0.01451 0.42132 2.92398
68 3FS8 ACO 0.00584 0.44899 2.9304
69 3FS8 TDR 0.009324 0.43808 2.9304
70 1JAC AMG 0.0004176 0.49973 3.00752
71 3CV2 OXL 0.00002386 0.5243 3.13589
72 1T26 GBD 0.001596 0.48231 3.13589
73 1T26 NAI 0.001596 0.48231 3.13589
74 3B9Z CO2 0.001776 0.43446 3.13589
75 2VJJ RAM GLC GAL NAG NAG GLC 0.0144 0.41682 3.13589
76 4WBD CIT 0.005531 0.40775 3.13589
77 2GDZ NAD 0.008952 0.4073 3.13589
78 2Q8H TF4 0.02089 0.40599 3.13589
79 3U1T MLI 0.01222 0.40414 3.13589
80 2H6B 3C4 0.004037 0.44433 3.2
81 1ZDU P3A 0.04399 0.40405 3.26531
82 2X2T GAL NGA 0.01291 0.41622 3.26797
83 3BHO B4P 0.004683 0.44638 3.36538
84 1Z6K OAA 0.004682 0.41849 3.41297
85 4C0C WVH 0.004483 0.43483 3.42612
86 1VBH PEP 0.00006586 0.51402 3.48432
87 2NLI FMN 0.001067 0.46611 3.48432
88 2NLI LAC 0.001067 0.46611 3.48432
89 3CXO 3LR 0.0003094 0.46484 3.48432
90 2AMV BIN 0.01683 0.44403 3.48432
91 3CXO 1N5 0.00566 0.41666 3.48432
92 3TO7 COA 0.0005916 0.46566 3.62319
93 4B16 NAG 0.02001 0.41418 3.7594
94 1QJC PNS 0.001361 0.46369 3.79747
95 2QIA U20 0.003218 0.44745 3.81679
96 1Y1A GSH 0.02888 0.4127 3.82514
97 2AEB ABH 0.000085 0.49456 3.83275
98 3O03 NAP 0.00186 0.46061 3.83275
99 2IMP NAI 0.004813 0.45392 3.83275
100 2IMP LAC 0.0003571 0.4476 3.83275
101 1RY2 AMP 0.001065 0.43853 3.83275
102 1ZUI SKM 0.01645 0.43734 3.83275
103 1V5F FAD 0.03438 0.43348 3.83275
104 1V5F TPP 0.03438 0.43348 3.83275
105 2X0K PPV 0.0002514 0.41581 3.83275
106 2JL1 NAP 0.03545 0.40391 3.83275
107 1Y42 TYR 0.005027 0.40371 3.83275
108 4IOK XPO 0.007184 0.40256 3.83275
109 3GJ4 GDP 0.02103 0.40186 3.83275
110 3O03 GCO 0.003465 0.40124 3.83275
111 2AWN ADP 0.01115 0.40046 3.83275
112 1SS4 GSH 0.00002433 0.58818 3.92157
113 2PNZ UDP 0.00035 0.45768 4.18118
114 1P9B HDA 0.001033 0.43763 4.18118
115 3AWJ COA 0.009432 0.42716 4.18118
116 1RYD GLC 0.003296 0.42292 4.18118
117 3WLE NAD 0.03213 0.41357 4.18118
118 3EC1 GDP 0.01779 0.40786 4.18118
119 2QQF A1R 0.007218 0.40556 4.18118
120 4GYW UDP 0.01247 0.40386 4.18118
121 4JCA CIT 0.001912 0.46616 4.19162
122 2BLE 5GP 0.00007943 0.52242 4.35967
123 2ZE3 AKG 0.004771 0.4101 4.36364
124 1XE7 GUN 0.008235 0.42573 4.4335
125 1HFA PIO 0.0009085 0.49795 4.52962
126 1O9U ADZ 0.00407 0.44062 4.52962
127 1GQY ACP 0.004573 0.43334 4.52962
128 1YOE RIB 0.002388 0.42913 4.52962
129 2W8Q SIN 0.006957 0.41511 4.52962
130 1FIQ MTE 0.007721 0.4099 4.52962
131 1FIQ SAL 0.008882 0.4099 4.52962
132 3HQP OXL 0.00008266 0.50203 4.60922
133 1GSA ADP 0.000617 0.47449 4.87805
134 1PIG AGL GLC HMC AGL GLC BGC 0.01031 0.45049 4.87805
135 1GSA GSH 0.003037 0.43913 4.87805
136 3SQG COM 0.01075 0.42798 4.87805
137 1C0I BE2 0.008484 0.42387 4.87805
138 1C0I FAD 0.008484 0.42387 4.87805
139 4USQ FAD 0.007664 0.41487 4.87805
140 3Q3C NAD 0.01858 0.41386 4.87805
141 2J62 GSZ 0.02171 0.40745 4.87805
142 2C7G FAD 0.02945 0.40713 4.87805
143 1TI7 NAP 0.0293 0.40688 4.87805
144 2C7G ODP 0.02922 0.40661 4.87805
145 3S9K CIT 0.01097 0.42956 5.08475
146 1JWY ADP 0.004062 0.43796 5.22648
147 1D8T GDP 0.009699 0.41959 5.22648
148 1A5Z OXM 0.01301 0.40915 5.22648
149 3IHB TRS 0.0001866 0.53702 5.57491
150 3VCA PRO 0.0001071 0.47438 5.57491
151 1RYI GOA 0.005631 0.45718 5.57491
152 2YVF NAD 0.02477 0.41367 5.57491
153 2YVF FAD 0.02399 0.41367 5.57491
154 1P7T PYR 0.000004513 0.56456 5.60876
155 2HVK TBA 0.0003957 0.46247 5.64516
156 4EKV BTN 0.002799 0.43167 5.66038
157 1Z0A GDP 0.01944 0.40535 5.74713
158 2OQ2 A3P 0.03771 0.40413 5.74713
159 4DN8 BMA 0.0004655 0.45944 5.76923
160 1QF5 GDP 0.009542 0.46024 5.92335
161 4TSK NDP 0.007298 0.43454 5.92335
162 1SAY PYR 0.0313 0.42096 5.92335
163 1QF5 RPL 0.02195 0.40771 5.92335
164 2I4O ATP 0.01493 0.40665 5.92335
165 4M5P 23W 0.01562 0.40544 5.92335
166 4M5P MLA 0.03718 0.40033 5.92335
167 3TA2 AKG 0.0007013 0.45055 5.9322
168 1QDS PGA 0.0008387 0.423 5.9761
169 3OIG NAD 0.0007656 0.4791 6.01504
170 3OIG IMJ 0.0003627 0.46802 6.01504
171 2BGM NAJ 0.0009445 0.47351 6.11511
172 1YZG GDP 0.01825 0.40499 6.14525
173 1Z0F GDP 0.02236 0.40039 6.14525
174 3H86 AP5 0.002551 0.44666 6.25
175 4G1V FAD 0.01043 0.44494 6.27178
176 4W6Z ETF 0.003701 0.44262 6.27178
177 2YBQ UP2 0.009032 0.41412 6.27178
178 5DRN 5CT 0.02775 0.40331 6.27178
179 1R0X ATP 0.0002247 0.47653 6.29371
180 1OFH ADP 0.0009491 0.44051 6.32184
181 3FMI KAP 0.01398 0.42397 6.3745
182 3VKX T3 0.0007007 0.43737 6.51341
183 1JGS SAL 0.002025 0.47572 6.52174
184 3TKA CTN 0.005477 0.4636 6.62021
185 1Q3Q ANP 0.004677 0.44304 6.62021
186 1Q19 APC 0.02723 0.40818 6.62021
187 2QEN ADP 0.02984 0.40104 6.62021
188 3RG9 WRA 0.006305 0.46431 6.66667
189 1IN4 ADP 0.01168 0.42333 6.88623
190 1YOA FMN 0.01406 0.43068 6.91824
191 2PAR TMP 0.002953 0.44113 6.96517
192 4L80 OXL 0.0000008783 0.60489 6.96864
193 3TFC PEP 0.00226 0.41761 6.96864
194 2VOH CIT 0.004675 0.43068 7.00637
195 3K3G MMU 0.0003904 0.45154 7.05882
196 2XBP ATP 0.005727 0.43162 7.07965
197 1U7Z PMT 0.03502 0.41592 7.07965
198 1LYX PGA 0.001062 0.405 7.25806
199 1JA9 NDP 0.003222 0.45705 7.31707
200 1IHU AF3 0.003986 0.45373 7.31707
201 1IHU ADP 0.004284 0.45373 7.31707
202 1JQN DCO 0.00006222 0.43443 7.31707
203 1JA9 PYQ 0.003078 0.4247 7.31707
204 1MG1 MAL 0.002965 0.41592 7.31707
205 4KCF AKM 0.005893 0.40594 7.31707
206 4KCF FMN 0.01558 0.40527 7.31707
207 2BNE U5P 0.0002859 0.47295 7.46888
208 1Y63 ADP 0.01864 0.4034 7.6087
209 3VHZ L2P GLC MAN SGA 0.004377 0.45013 7.63359
210 3CL7 HYN 0.0005173 0.4492 7.66551
211 2FNU PMP UD1 0.04712 0.40862 7.66551
212 2VQ5 HBA 0.0116 0.40515 7.66551
213 4CMF PXG 0.00009898 0.51068 8.01394
214 1OMZ UD2 0.001967 0.4491 8.01394
215 2E5V FAD 0.03739 0.41642 8.01394
216 3UYK 0CX 0.04345 0.41115 8.01394
217 4HZX G39 0.01992 0.40271 8.01394
218 4OYA 1VE 0.001809 0.48176 8.08511
219 2XI7 XI7 0.01245 0.43352 8.15217
220 1FZQ GDP 0.01747 0.40547 8.28729
221 2Q37 3AL 0.006367 0.40489 8.28729
222 4IP7 FLC 0.00003952 0.47532 8.36237
223 1H16 PYR 0.002552 0.44213 8.36237
224 1SSQ CYS 0.01519 0.41343 8.36237
225 2F01 BTQ 0.03334 0.40965 8.36237
226 2F01 BTN 0.03378 0.40939 8.36237
227 1KWK GAL 0.0002475 0.40358 8.36237
228 1H8G CHT 0.007707 0.44468 8.42105
229 1U3G THF 0.006292 0.44947 8.46561
230 4Q3F TLA 0.003689 0.40385 8.54701
231 3ZGE ASP 0.01279 0.4095 8.7108
232 3CQD ATP 0.01264 0.40907 8.7108
233 1UJ2 C5P 0.0294 0.41178 8.73016
234 1GXU 2HP 0.02224 0.40582 8.79121
235 1XX4 BAM 0.0001059 0.47457 8.81226
236 3FPZ AHZ 0.006734 0.44728 9.05923
237 2XDQ MGX 0.01148 0.4187 9.05923
238 3PNL ADP 0.003917 0.41121 9.05923
239 2XZ9 PYR 0.00006662 0.47909 9.40767
240 4U36 TNR 0.001551 0.4304 9.58333
241 4BI7 PGA 0.001112 0.40723 10.1167
242 1WRA PC 0.006284 0.41709 10.3896
243 3S5W FAD 0.04925 0.41046 10.453
244 3IB9 BTN 0.001941 0.44368 10.8014
245 2ZO9 MLI 0.001863 0.40753 10.8014
246 1JUV NDP 0.0107 0.40017 10.8808
247 3I8T LBT 0.003672 0.40917 10.9756
248 1I2B USQ 0.006978 0.46174 11.1498
249 1I2B UPG 0.006978 0.46174 11.1498
250 1I2B NAD 0.006978 0.46174 11.1498
251 4OK9 HIS 0.0009473 0.42921 11.4094
252 2G50 PYR 0.000104 0.49599 11.4983
253 2OG2 MLI 0.002014 0.44333 11.4983
254 3B9Q MLI 0.003806 0.42833 11.4983
255 1ML4 PAL 0.0001093 0.40384 11.4983
256 1NME 159 0.003445 0.40134 11.6438
257 2Q3M MLA 0.006971 0.42925 11.6564
258 4KCT PYR 0.00004794 0.46043 11.8467
259 4WZA ACP 0.01949 0.4491 11.8467
260 1EDO NAP 0.01217 0.43113 11.8852
261 4AF5 CIT 0.002952 0.42498 12.1053
262 4FGC PQ0 0.007609 0.40168 12.7273
263 3FRK TQP 0.0064 0.45643 12.892
264 4INI AMP 0.01718 0.40704 13.0769
265 1NXJ GLV 0.00007171 0.46996 13.1148
266 2X61 CH 0.000234 0.48371 13.1783
267 2X61 NGA GAL SIA 0.001491 0.46481 13.1783
268 3F81 STT 0.003547 0.44352 13.2404
269 1H0C AOA 0.008597 0.41099 13.2404
270 4C2W ANP 0.01132 0.41333 13.4615
271 1ZFJ IMP 0.004853 0.46087 13.9373
272 3GE7 AFQ 0.01598 0.40057 13.9373
273 1T0S BML 0.01842 0.40208 13.9535
274 1KOL NAD 0.03477 0.41743 14.2857
275 1MR3 G3D 0.0237 0.40031 14.9171
276 1UQX MMA 0.001025 0.4375 15.0442
277 1NVU GTP 0.001614 0.46172 15.0602
278 1KC7 PPR 0.00003009 0.5279 15.331
279 1KO8 6PG 0.02884 0.40694 15.4286
280 2W9S NDP 0.03132 0.40972 16.1491
281 1DL7 NCH 0.04156 0.40524 16.9643
282 3KJS DQ1 0.03464 0.41842 17.0732
283 3KJS NAP 0.03303 0.41352 17.0732
284 4GQB 0XU 0.01045 0.42478 18.1818
285 2FWP ICR 0.0003436 0.4717 19.6721
286 2FWP CIT 0.001445 0.44076 19.6721
287 2VKL MLT 0.01932 0.41497 23.3333
288 2V5E SCR 0.00529 0.44368 23.7624
289 4C2V YJA 0.03672 0.41544 25
290 1IZC PYR 0.00000006082 0.56363 44.2509
Pocket No.: 2; Query (leader) PDB : 2V5K; Ligand: OXM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2v5k.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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