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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 with APoc: 240
This union binding pocket(no: 1) in the query (biounit: 2v5k.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 4D81 ADP None
2 4E03 ADP None
3 3P48 DUP None
4 4KBS PX2 1.39535
5 1C9K 5GP 1.66667
6 3NOJ PYR 1.68067
7 2PID YSA 1.74216
8 2Y65 ADP 1.74216
9 2H29 DND 1.74216
10 3P7N FMN 1.93798
11 5H68 AGS 2.09059
12 4UTG ANP 2.09059
13 4KVL PLM 2.09059
14 1X8J A3P 2.09059
15 1JGT CMA 2.09059
16 1JGT APC 2.09059
17 1J99 AND 2.09059
18 2Z5F A3P 2.34899
19 4V0K GDP 2.36686
20 4TL6 ANP 2.37154
21 1GQG DCD 2.43902
22 1NJF ADP 2.43902
23 1NJF AGS 2.43902
24 4NE2 ADP 2.43902
25 5E2N V14 2.43902
26 1G3M PCQ 2.43902
27 1G3M A3P 2.43902
28 3LRE ADP 2.43902
29 4IEE AGS 2.43902
30 3QVV 3QV 2.43902
31 1FP6 ADP 2.43902
32 1F6B GDP 2.52525
33 6C6O ENG 2.5641
34 5T9F TYR 2.58303
35 5T9F NAP 2.58303
36 1D8C GLV 2.78746
37 2PA4 UPG 2.78746
38 5W3K NDP 2.78746
39 5W3K 9TY 2.78746
40 3H22 B53 2.78746
41 3A4X NAG NAG NAG NDG 2.78746
42 3A8T ATP 2.78746
43 1KK1 GNP 2.78746
44 5O4J 9KH 2.91971
45 5O4J PJL 2.91971
46 5O4J SAH 2.91971
47 5EYG NAP 3.01887
48 3CV2 OXL 3.13589
49 1W7J ADP BEF 3.13589
50 3NUB UD0 3.13589
51 4WBD CIT 3.13589
52 1EE0 CAA 3.13589
53 1Q20 A3P 3.13589
54 1Q20 PLO 3.13589
55 5A89 FMN 3.20513
56 2B99 RDL 3.20513
57 1ZDU P3A 3.26531
58 4NTO 1PW 3.38164
59 1Z6K OAA 3.41297
60 1VBH PEP 3.48432
61 2AMV BIN 3.48432
62 5I0H ADP BEF 3.48432
63 1C7O PPG 3.48432
64 3C3N FMN 3.48432
65 4EIL NDP 3.48432
66 2BEK ATP 3.50195
67 1ZUI SKM 3.83275
68 5M7P ADP 3.83275
69 1LVK MNT BEF 3.83275
70 3NC9 TR3 3.83275
71 4B47 GDP 3.83275
72 2PI8 NAG NAG NAG NAG NAG NAG 3.83275
73 4S3F 43W 3.83275
74 4ZKD GDP 3.83275
75 2JL1 NAP 3.83275
76 1CX4 CMP 3.83275
77 3GJ4 GDP 3.83275
78 3X27 TRP 3.83275
79 2AWN ADP 3.83275
80 5BYK A3P 3.861
81 5BYK OAQ 3.861
82 3ITJ FAD 4.18118
83 3AWJ COA 4.18118
84 5JCA FAD 4.18118
85 3HWW AKG 4.18118
86 3WLE NAD 4.18118
87 2D3M COA 4.18118
88 5H7J GCP 4.18118
89 3EC1 GDP 4.18118
90 4WJT NAG 4.19162
91 1YRO GDU 4.1958
92 5FG3 GDP 4.49438
93 1GQY ACP 4.52962
94 4PVV HO4 4.52962
95 1G7C 5GP 4.52962
96 3WYA GDP 4.52962
97 1D2E GDP 4.52962
98 5XET ME8 4.52962
99 1P3D ANP 4.52962
100 5LB3 ADP 4.52962
101 3HQP OXL 4.60922
102 5BXQ GDP 4.72441
103 2NV4 SAM 4.7619
104 1PIG AGL GLC HMC AGL GLC BGC 4.87805
105 4J0Q GDP 4.87805
106 2J62 GSZ 4.87805
107 1TI7 NAP 4.87805
108 4WOP CTP 4.88889
109 1M5W DXP 4.93827
110 1XEX ATP 4.94506
111 4QDI ATP 5.08475
112 6CLV 6MB 5.22648
113 1D8T GDP 5.22648
114 5WX3 COA 5.22648
115 5EZ7 FAD 5.22648
116 1D6H COA 5.22648
117 3U6K GDP 5.22648
118 4PC3 GDP 5.22648
119 1W5T ANP 5.22648
120 5JBQ GDP 5.22648
121 1FQJ GDP 5.44218
122 1FQK GDP 5.44218
123 4X17 SIA SIA 5.51471
124 1XTT U5P 5.55556
125 4W93 3L9 5.57491
126 4MXP DB4 5.57491
127 4QYS PLP SEP 5.57491
128 1AQU A3P 5.57491
129 1P7T PYR 5.60876
130 5W8Q BU4 5.64103
131 2OQ2 A3P 5.74713
132 1Z0A GDP 5.74713
133 2X77 GDP 5.82011
134 1QF5 GDP 5.92335
135 1QF5 RPL 5.92335
136 1SAY PYR 5.92335
137 2I4O ATP 5.92335
138 1P72 ADP 5.92335
139 5U32 GDP 5.9322
140 1YZG GDP 6.14525
141 1Z0F GDP 6.14525
142 3H86 AP5 6.25
143 4PFO ADP 6.27178
144 2VB6 ADP BEF 6.27178
145 1WD4 AHR 6.27178
146 1XNG DND 6.34328
147 5TSH ANP 6.46258
148 5ZBR ANP 6.62021
149 1Q19 APC 6.62021
150 6B4K ANP 6.62021
151 2QEN ADP 6.62021
152 3RG9 WRA 6.66667
153 4QOS ADP 6.79245
154 1IN4 ADP 6.88623
155 1PVN MZP 6.91489
156 4L9Z COA 6.96864
157 4L80 OXL 6.96864
158 4L9Z OXL 6.96864
159 5WS9 ATP 6.96864
160 5WS9 OXL 6.96864
161 5W75 GDP 6.96864
162 4XDA ADP 6.96864
163 1SQ5 ADP 6.96864
164 2VOH CIT 7.00637
165 1B7T ADP 7.05128
166 1U7Z PMT 7.07965
167 1UNQ 4IP 7.2
168 1IHU ADP 7.31707
169 1IHU AF3 7.31707
170 1JQN DCO 7.31707
171 4YLG GDP 7.51445
172 1Y63 ADP 7.6087
173 5GXU FAD 7.66551
174 2FNU PMP UD1 7.66551
175 6C4M NAP 7.66551
176 1QHH ATP 7.78443
177 1A4R GDP 7.8534
178 1KK8 BEF ADP 7.91367
179 2E5V FAD 8.01394
180 3UYK 0CX 8.01394
181 5YGE ACO 8.04598
182 5O74 GDP 8.12183
183 2QQ0 ADP 8.15217
184 2QQ0 TMP 8.15217
185 1FZQ GDP 8.28729
186 4IP7 FLC 8.36237
187 4ZG4 VO4 ADP 8.36237
188 2GKS ADP 8.36237
189 4LC1 GDP 8.36237
190 1XX6 ADP 8.37696
191 5N69 ADP 8.7108
192 1UJ2 ADP 8.73016
193 1UJ2 C5P 8.73016
194 2ZTS ADP 8.76494
195 1GXU 2HP 8.79121
196 1ML6 GBX 9.04977
197 1G4U GDP 9.05923
198 1G7S GDP 9.05923
199 2XZ9 PYR 9.40767
200 2ZR9 DTP 9.40767
201 4YRY FAD 9.42029
202 5E5U MLI 9.84848
203 3S5W FAD 10.453
204 2QN6 GDP 10.7527
205 6HKE MLT 10.8014
206 5KDO GDP 10.8108
207 1M7G ADP 10.9005
208 2G50 PYR 11.4983
209 3B9Q MLI 11.4983
210 2OG2 MLI 11.4983
211 4XGU ADP 11.7925
212 4KCT PYR 11.8467
213 4WZA ACP 11.8467
214 4WZA ADP 11.8467
215 5JCP GDP ALF 11.8467
216 5EYK 5U5 11.8644
217 2F3R G5P 12.0773
218 4XF6 ADP 12.4542
219 4XF6 LIP 12.4542
220 4XF6 INS 12.4542
221 1HE1 GDP 12.5
222 3FRK TQP 12.892
223 4INI AMP 13.0769
224 5MEX SZZ 13.2404
225 4C2W ANP 13.4615
226 1ZJ6 G3D 13.9037
227 1KOL NAD 14.2857
228 1MR3 G3D 14.9171
229 1KC7 PPR 15.331
230 1KO8 6PG 15.4286
231 2W9S NDP 16.1491
232 2OM2 GDP 16.6667
233 3KJS DQ1 17.0732
234 3KJS NAP 17.0732
235 1OW3 GDP 19.6891
236 5HPY GDP 20.5405
237 4C2V YJA 25
238 4WK1 2BA 31.0078
239 4RLE 2BA 33.3333
240 1IZC PYR 44.2509
Pocket No.: 2; Query (leader) PDB : 2V5K; Ligand: OXM; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2V5K; Ligand: OXM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2v5k.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2V5K; Ligand: OXM; Similar sites found with APoc: 67
This union binding pocket(no: 4) in the query (biounit: 2v5k.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1FHW I5P None
2 1T8U UAP SGN IDS SGN 1.10294
3 5XQL C2E 1.39373
4 1Y3A GDP 2.09059
5 1BH2 GSP 2.09059
6 1SKQ GDP 2.09059
7 5OCQ 9RN G4S 9RN G4S 2.10526
8 5J1J ANP 2.10526
9 1WOQ BGC 2.24719
10 4NE2 SH2 2.43902
11 6CRK GDP 2.43902
12 3QVV A3P 2.43902
13 2AQJ FAD 2.78746
14 2AQJ TRP 2.78746
15 3ZL8 ADP 2.78746
16 2C6Q IMP 2.78746
17 5BN3 ADP 2.78746
18 2YFO GLA 2.78746
19 2YFO GAL 2.78746
20 2ZFI ADP 3.00546
21 5E4R NAP 3.13589
22 4X7Y SAH 3.13589
23 3MGB PAP 3.13589
24 2NUN ADP 3.13589
25 6H5E ANP 3.13589
26 3SMA ACO 3.14685
27 5A89 ADP 3.20513
28 3MHP FAD 3.48432
29 5WRJ A3P 4.18118
30 5WRI A3P 4.18118
31 1VG9 GDP 4.32432
32 3BFX A3P 4.52962
33 3WY9 GDP 4.52962
34 1QHG ATP 4.52962
35 1FKB RAP 4.6729
36 2RCU BUJ 4.87805
37 2XTZ GSP 4.87805
38 4G5G GDP 5.22648
39 4P3Y GDP 5.22648
40 2XVF FAD 5.22648
41 2XN2 GLA 5.22648
42 2BVN GNP 5.22648
43 5K5Z ANP 5.57491
44 2IU8 PLM 5.57491
45 4BQS ADP 5.68182
46 6GEH FAD 5.85938
47 2D7C GTP 5.98802
48 3TNF GNP 6.32184
49 2HV8 GTP 6.39535
50 5SZH GNP 6.40394
51 4C4P GNP 6.54206
52 5W7Q GDP 6.70241
53 2DX7 CIT 7.01754
54 4HI0 GDP 7.03518
55 3ZKK XYP XYP XYP XYP 7.66551
56 6F3M NAD 7.66551
57 2WMO GTP 7.89474
58 5IQT 6CU 7.93651
59 5IQT AKG 7.93651
60 2FAH GDP 8.01394
61 2QZS GLC 8.36237
62 2QZS ADP 8.36237
63 2QZS 250 8.36237
64 5XLY C2E 9.77444
65 2HCJ GDP 10.8108
66 3N5C GDP 13.5802
67 1RE0 GDP 15.8537
Pocket No.: 5; Query (leader) PDB : 2V5K; Ligand: OXM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2v5k.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2V5K; Ligand: OXM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2v5k.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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