Receptor
PDB id Resolution Class Description Source Keywords
2VWT 1.93 Å EC: 4.1.2.20 CRYSTAL STRUCTURE OF YFAU, A METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERICHIA COLI K12 - MG-PYRUVATE PRODUCT C OMPLEX ESCHERICHIA COLI LYASE (BETA/ALPHA)8 BARREL 2-KETO-3-DEOXY SUGAR ALDOLASE ESCHERICHIA COLI K-12 PROTEIN YFAU DEGRADATION OF HOMOPROTOCATECHUATE PYRUVATE CLASS II ALDOLASE
Ref.: CRYSTAL STRUCTURE AND FUNCTIONAL ASSIGNMENT OF YFAU METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERIC K12. BIOCHEMISTRY V. 47 9955 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL C:1258;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:301;
B:301;
C:301;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PO4 A:1257;
B:1257;
C:1257;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
PYR A:302;
B:302;
C:302;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
88.062 C3 H4 O3 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VWT 1.93 Å EC: 4.1.2.20 CRYSTAL STRUCTURE OF YFAU, A METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERICHIA COLI K12 - MG-PYRUVATE PRODUCT C OMPLEX ESCHERICHIA COLI LYASE (BETA/ALPHA)8 BARREL 2-KETO-3-DEOXY SUGAR ALDOLASE ESCHERICHIA COLI K-12 PROTEIN YFAU DEGRADATION OF HOMOPROTOCATECHUATE PYRUVATE CLASS II ALDOLASE
Ref.: CRYSTAL STRUCTURE AND FUNCTIONAL ASSIGNMENT OF YFAU METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERIC K12. BIOCHEMISTRY V. 47 9955 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2VWT - PYR C3 H4 O3 CC(=O)C(=O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2VWT - 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: PYR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 KIV 0.411765 0.785714
5 AAE 0.411765 0.625
6 2KT 0.411765 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VWT; Ligand: PYR; Similar sites found: 215
This union binding pocket(no: 1) in the query (biounit: 2vwt.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.0005972 0.48528 None
2 1BTN I3P 0.001456 0.47593 None
3 1IS3 LAT 0.001108 0.43263 None
4 2VOH CIT 0.005305 0.43037 None
5 1Y7P RIP 0.002039 0.42915 None
6 1UO4 PIH 0.006011 0.42444 None
7 4EXO PYR 0.003962 0.4164 None
8 1Y75 NAG 0.0002516 0.41347 None
9 1PTR PRB 0.005676 0.40259 None
10 1J99 AND 0.01024 0.44163 0.749064
11 2V5E SCR 0.00602 0.42441 1
12 2Y65 ADP 0.01114 0.40416 1.1236
13 3FPZ AHZ 0.01244 0.46179 1.49813
14 3F81 STT 0.01269 0.40092 1.63934
15 4LWM MHO 0.0117 0.43761 1.84332
16 2GDZ NAD 0.0005365 0.49416 1.87266
17 1O9U ADZ 0.0004511 0.46794 1.87266
18 1T3D CYS 0.002929 0.41477 1.87266
19 1H8G CHT 0.009494 0.42388 2.10526
20 2V7T SAH 0.01404 0.46292 2.24719
21 4QVH FLC 0.00315 0.45209 2.24719
22 2PTZ PAH 0.001526 0.45075 2.24719
23 2BO4 FLC 0.001228 0.43074 2.24719
24 3ICV NAG 0.01059 0.42245 2.24719
25 4C2G ALA ALA ALA ALA 0.0001701 0.42059 2.24719
26 2OWZ CIT 0.001051 0.41911 2.24719
27 1PEA ACM 0.005541 0.40996 2.24719
28 3CEV ARG 0.0002599 0.40827 2.24719
29 3KJI ADP 0.002631 0.43999 2.3622
30 3SBZ MLI 0.006619 0.41403 2.38095
31 3MAG 3MA 0.0001527 0.50178 2.62172
32 3TKA CTN 0.001652 0.47967 2.62172
33 1RZM E4P 0.0008293 0.43796 2.62172
34 1FDJ 2FP 0.01026 0.40871 2.62172
35 1FDJ 13P 0.01471 0.40327 2.62172
36 2ZWS PLM 0.02658 0.40088 2.62172
37 3UBW 6SP 0.0001815 0.51027 2.68199
38 3QDV A2G 0.002004 0.43803 2.7972
39 3QDT A2G GAL 0.001622 0.43354 2.7972
40 3QDX A2G GAL 0.001292 0.4205 2.7972
41 3QDW A2G 0.004966 0.41981 2.7972
42 3QDY A2G GAL 0.007084 0.40523 2.7972
43 1JN2 SFP 0.04108 0.4043 2.95359
44 3O03 GCO 0.0009953 0.45208 2.99625
45 4N02 FNR 0.02024 0.43725 2.99625
46 4DXJ IPE 0.001953 0.43564 2.99625
47 2ZJ3 G6P 0.004847 0.43393 2.99625
48 3DAG FEG 0.01044 0.42647 2.99625
49 1R37 ETX 0.0008506 0.42434 2.99625
50 2ZJ5 ADP 0.0006444 0.41612 2.99625
51 1P9P SAH 0.01446 0.4152 2.99625
52 4DXJ 0M9 0.006901 0.41403 2.99625
53 1Y42 TYR 0.0005098 0.41119 2.99625
54 1BG2 ADP 0.009057 0.40533 2.99625
55 3CBG FER 0.003669 0.42589 3.01724
56 3CBG 4FE 0.006037 0.42435 3.01724
57 1XX4 BAM 0.001503 0.40096 3.06513
58 2H6B 3C4 0.0217 0.43708 3.2
59 3VPD BUA 0.0001568 0.52314 3.37079
60 2XZ9 PYR 0.0000794 0.47553 3.37079
61 3L24 GOA 0.0003165 0.47505 3.37079
62 1HFA PIO 0.003489 0.46678 3.37079
63 4M5P MLA 0.001151 0.45927 3.37079
64 3HQP OXL 0.0004583 0.45657 3.37079
65 1TDF FAD 0.007262 0.45615 3.37079
66 1TDF NAP 0.0155 0.45345 3.37079
67 4RNV HBA 0.001838 0.44931 3.37079
68 2C31 TZD 0.02119 0.44677 3.37079
69 2C31 ADP 0.0207 0.44677 3.37079
70 1GAD NAD 0.004711 0.44441 3.37079
71 4RNV FMN 0.002303 0.44374 3.37079
72 3VPD CIT 0.004897 0.42877 3.37079
73 3UDG TMP 0.005185 0.41894 3.37079
74 1Z42 HBA 0.02565 0.40662 3.37079
75 2AEB ABH 0.04281 0.40575 3.37079
76 4JWX 1N4 0.00109 0.40048 3.37079
77 1RYI GOA 0.02785 0.4018 3.40314
78 1WGC SIA GAL BGC 0.007963 0.41851 3.50877
79 3AB3 GDP 0.02245 0.40398 3.65854
80 3I7S PYR 0.001556 0.43434 3.74532
81 4CIB 7UZ 0.0005093 0.42278 3.74532
82 1H16 PYR 0.006458 0.40701 3.74532
83 3A8U PLP 0.006661 0.40636 3.74532
84 2VVG ADP 0.0101 0.40308 3.74532
85 3R51 MMA 0.006371 0.4148 3.75
86 2YD6 FLC 0.0001021 0.55063 3.77358
87 3NOJ PYR 0.01832 0.40427 3.78151
88 2X2T GAL NGA 0.005856 0.4165 3.92157
89 1SC3 MLI 0.009178 0.40025 3.93258
90 2BZ1 TAU 0.00004096 0.54466 4.08163
91 4JEJ 1GP 0.00007038 0.40751 4.09836
92 4O8A 2OP 0.0003603 0.47245 4.11985
93 3IHB TRS 0.004236 0.4664 4.11985
94 3IHB GLU 0.001399 0.42835 4.11985
95 3ZOK NAD 0.02482 0.41234 4.11985
96 3B8I OXL 0.01414 0.40637 4.11985
97 4LIT AKG 0.00173 0.40428 4.11985
98 1NF8 BOG 0.004286 0.40776 4.34783
99 1I0Z OXM 0.000208 0.48347 4.49438
100 3C1O NAP 0.001698 0.46233 4.49438
101 2WQP WQP 0.002863 0.45474 4.49438
102 1X54 4AD 0.002878 0.4515 4.49438
103 4WBD CIT 0.006 0.41601 4.49438
104 4M51 BEZ 0.007484 0.40418 4.49438
105 4DVE BTN 0.0004809 0.4655 4.54545
106 3PNA CMP 0.0003798 0.40149 4.54545
107 1SS4 GSH 0.001969 0.47072 4.57516
108 1H8P PC 0.006585 0.41414 4.58716
109 2BLE 5GP 0.002865 0.48556 4.86891
110 1IYE PGU 0.00144 0.47487 4.86891
111 2Q3M MLA 0.0111 0.41027 4.86891
112 3ZGE ASP 0.008267 0.40226 4.86891
113 2W8Q SIN 0.006138 0.40115 4.86891
114 1Y1A GSH 0.001594 0.46422 4.91803
115 1JGS SAL 0.002476 0.45375 5.07246
116 1P7T PYR 0.00001603 0.50872 5.24345
117 3BLI PYR 0.00429 0.40775 5.24345
118 3SQG COM 0.01689 0.4026 5.24345
119 1NME 159 0.003132 0.42907 5.43478
120 4F8L GAL 0.009834 0.4231 5.51724
121 1QDS PGA 0.0002228 0.40355 5.57769
122 3E4O SIN 0.0003987 0.45931 5.61798
123 1RRC ADP 0.004859 0.43745 5.61798
124 3DDN HPV 0.001932 0.42965 5.61798
125 2YIV NBN 0.00181 0.42362 5.61798
126 1YOA FMN 0.0009714 0.47449 5.66038
127 1Y4Z PCI 0.002642 0.41667 5.77778
128 4UOH ADP 0.0119 0.40096 5.96026
129 4R33 SAH 0.005921 0.44754 5.99251
130 4R33 TRP 0.005921 0.44754 5.99251
131 1GPJ CIT 0.002388 0.4072 5.99251
132 4A3X LAT 0.009351 0.40708 6.1674
133 1NU4 MLA 0.003495 0.4461 6.18557
134 2XDQ MGX 0.0004942 0.46612 6.36704
135 2G50 PYR 0.0005482 0.45621 6.36704
136 1MG1 MAL 0.002832 0.44844 6.36704
137 2CW6 3HG 0.004142 0.42346 6.36704
138 3DX5 DHB 0.0001034 0.41967 6.36704
139 4RJK PYR 0.003387 0.41941 6.36704
140 2Q1A 2KT 0.001989 0.41082 6.36704
141 1XE7 GUN 0.005795 0.41671 6.40394
142 2W1A TSA 0.005164 0.41964 6.74157
143 3HZL 6PC 0.008237 0.40963 6.74157
144 4AF5 CIT 0.0009953 0.42164 6.84211
145 1H9G COA MYR 0.002983 0.45389 6.99588
146 2VDJ HSE 0.006986 0.4055 7.11611
147 4NAO AKG 0.004934 0.40517 7.11611
148 3WUC GLC GAL 0.006493 0.40011 7.29927
149 2EFJ SAH 0.0005872 0.47198 7.49064
150 1JBW ACQ 0.003566 0.46566 7.49064
151 1VBH PEP 0.0001667 0.4603 7.49064
152 1JBW TMF 0.02536 0.42406 7.49064
153 2XUM OGA 0.0009035 0.4222 7.49064
154 3P3N AKG 0.001123 0.41859 7.49064
155 4B7E OGA 0.0008774 0.41088 7.49064
156 5YAS FAC 0.001403 0.44484 7.7821
157 1R6D NAD 0.0443 0.41815 7.86517
158 3A1I UNU 0.0002404 0.40541 7.86517
159 4GYW UDP 0.004231 0.45344 8.2397
160 1KC7 PPR 0.00004939 0.51063 8.61423
161 3CL7 HYN 0.01256 0.42117 8.61423
162 1OMZ UD2 0.03179 0.42101 8.61423
163 1P72 THM 0.0003085 0.4191 8.61423
164 2NW9 FT6 0.005972 0.40842 8.61423
165 3I59 N6S 0.02954 0.40328 8.83534
166 2D37 NAD 0.02108 0.41453 9.09091
167 2D37 FMN 0.02462 0.40998 9.09091
168 1KSH GDP 0.01287 0.41254 9.13978
169 1D8C GLV 0.0000141 0.50879 9.3633
170 1U5V ATP 0.0007076 0.49337 9.3633
171 1V5F TPP 0.03178 0.45861 9.3633
172 1V5F FAD 0.03178 0.45861 9.3633
173 1Z6K OAA 0.004916 0.41235 9.3633
174 1YAG ATP 0.0007846 0.47639 9.6
175 2IZ1 ATR 0.0006736 0.4262 9.73783
176 1GJW GLC 0.002978 0.41446 9.73783
177 2WM1 13P 0.005692 0.41234 9.73783
178 2QLX RM4 0.000866 0.43716 10.1852
179 1UWZ THU 0.01674 0.40335 10.2941
180 4C4P GNP 0.02672 0.40857 10.4046
181 2HV8 GTP 0.02201 0.41273 10.4651
182 4BAS GNP 0.004815 0.43589 10.5528
183 3FMI KAP 0.02669 0.41017 10.757
184 2YVF FAD 0.006876 0.46648 10.8614
185 2YVF NAD 0.007084 0.46648 10.8614
186 1XHL NDP 0.002643 0.46339 10.8614
187 3WXM GTP 0.02031 0.40988 10.8614
188 1GXU 2HP 0.002921 0.44023 10.989
189 1WHT BZS 0.003385 0.4025 11.1111
190 2OG2 MLI 0.009869 0.40328 11.6105
191 3F8C HT1 0.001491 0.40242 11.9048
192 4JCA CIT 0.0007306 0.46884 11.976
193 4L80 OXL 0.000001599 0.57454 12.3596
194 3CV2 OXL 0.00007311 0.48761 12.3596
195 1E7S NAP 0.007641 0.44092 12.3596
196 1JQN DCO 0.0001727 0.42512 12.3596
197 2P1M IHP 0.02251 0.4105 12.5
198 1ULE GLA GAL NAG 0.00317 0.42068 12.6667
199 2Q37 3AL 0.0009602 0.41083 12.7072
200 9LDB OXM 0.004106 0.43248 12.7341
201 9LDT OXM 0.01214 0.40959 12.7341
202 4G1V FAD 0.005244 0.44362 13.1086
203 3NNF AKG 0.003224 0.40044 13.1086
204 4HVK PMP 0.001759 0.43765 13.4831
205 3ZLM ANP 0.006004 0.42773 13.8298
206 4KCT PYR 0.0004886 0.4241 13.8577
207 2XI7 XI7 0.00879 0.4256 14.6739
208 2I5F 5IP 0.009884 0.40337 14.6789
209 1G0V NAG 0.0001199 0.53311 19.3548
210 2O66 FLC 0.001917 0.40159 20
211 1H2K OGA 0.001037 0.4199 21.9512
212 4IP7 FLC 0.0003123 0.43979 22.4719
213 2FWP ICR 0.02572 0.41831 28.4153
214 2FWP CIT 0.02331 0.41607 28.4153
215 1IZC PYR 0.000001051 0.51188 28.4644
Pocket No.: 2; Query (leader) PDB : 2VWT; Ligand: PYR; 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: 2vwt.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2VWT; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2vwt.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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