Receptor
PDB id Resolution Class Description Source Keywords
2WNZ 1.85 Å EC: 4.1.3.3 STRUCTURE OF THE E192N MUTANT OF E. COLI N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE IN SPACE GROUP P21 C RYSTAL FORM I ESCHERICHIA COLI SUBSTRATE SPECIFICITY CARBOHYDRATE METABOLISM DIRECTED EVOPROTEIN ENGINEERING LYASE ALDOLASE SCHIFF BASE
Ref.: STRUCTURAL INSIGHTS INTO SUBSTRATE SPECIFICITY IN VARIANTS OF N-ACETYLNEURAMINIC ACID LYASE PRODUCED BY DIRECTED EVOLUTION. J.MOL.BIOL. V. 404 56 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2OP D:1296;
Valid;
none;
submit data
90.078 C3 H6 O3 C[C@@...
ETX C:1298;
D:1297;
Invalid;
Invalid;
none;
none;
submit data
90.121 C4 H10 O2 CCOCC...
LAC C:1297;
Valid;
none;
submit data
90.078 C3 H6 O3 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2WPB 2.05 Å EC: 4.1.3.3 CRYSTAL STRUCTURE OF THE E192N MUTANT OF E. COLI N- ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE AND T HE INHIBITOR (2R,3R)-2,3,4-TRIHYDROXY-N,N- DI PROPYLBUTANAMIDE IN SPACE GROUP P21 CRYSTAL FORM I ESCHERICHIA COLI SUBSTRATE SPECIFICITY CARBOHYDRATE METABOLISM PROTEIN ENGILYASE ALDOLASE SCHIFF BASE
Ref.: STRUCTURAL INSIGHTS INTO SUBSTRATE SPECIFICITY IN VARIANTS OF N-ACETYLNEURAMINIC ACID LYASE PRODUCED BY DIRECTED EVOLUTION. J.MOL.BIOL. V. 404 56 2010
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2WPB Ki = 1.3 mM ZZI C10 H21 N O4 CCCN(CCC)C....
2 2WNZ - LAC C3 H6 O3 C[C@H](C(=....
3 2XFW - PYR C3 H4 O3 CC(=O)C(=O....
4 2WKJ - PYR C3 H4 O3 CC(=O)C(=O....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2WPB Ki = 1.3 mM ZZI C10 H21 N O4 CCCN(CCC)C....
2 2WNZ - LAC C3 H6 O3 C[C@H](C(=....
3 2XFW - PYR C3 H4 O3 CC(=O)C(=O....
4 2WKJ - PYR C3 H4 O3 CC(=O)C(=O....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2WPB Ki = 1.3 mM ZZI C10 H21 N O4 CCCN(CCC)C....
2 2WNZ - LAC C3 H6 O3 C[C@H](C(=....
3 2XFW - PYR C3 H4 O3 CC(=O)C(=O....
4 2WKJ - PYR C3 H4 O3 CC(=O)C(=O....
5 4IMF - SI3 C11 H19 N O9 CC(=O)N[C@....
6 4IMG - NGF C11 H19 N O10 C([C@@H]([....
7 1F73 Ki = 4.1 mM HMN C11 H21 N O9 CC(=O)N[C@....
8 1F74 Ki = 0.9 mM NAY C11 H19 N O8 CC(=O)N[C@....
9 5KZD Ki = 0.39 mM RCJ C11 H21 N O9 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2OP; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 LAC 1 1
2 2OP 1 1
3 HBS 0.6 0.615385
4 HBR 0.6 0.615385
5 2RH 0.5 0.631579
6 TAR 0.5 0.611111
7 SRT 0.5 0.611111
8 TLA 0.5 0.611111
9 IPM 0.47619 0.631579
10 KIV 0.444444 0.625
11 LFC 0.434783 0.8
12 QFH 0.428571 0.631579
13 WTZ 0.428571 0.631579
14 23B 0.428571 0.631579
15 RAT 0.421053 0.611111
16 GAE 0.421053 0.611111
17 LGT 0.421053 0.611111
18 3LR 0.4 0.6
Ligand no: 2; Ligand: LAC; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 LAC 1 1
2 2OP 1 1
3 HBS 0.6 0.615385
4 HBR 0.6 0.615385
5 2RH 0.5 0.631579
6 TAR 0.5 0.611111
7 SRT 0.5 0.611111
8 TLA 0.5 0.611111
9 IPM 0.47619 0.631579
10 KIV 0.444444 0.625
11 LFC 0.434783 0.8
12 QFH 0.428571 0.631579
13 WTZ 0.428571 0.631579
14 23B 0.428571 0.631579
15 RAT 0.421053 0.611111
16 GAE 0.421053 0.611111
17 LGT 0.421053 0.611111
18 3LR 0.4 0.6
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2WPB; Ligand: ZZI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2wpb.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2WPB; Ligand: ZZI; 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: 2wpb.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2WPB; Ligand: ZZI; 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: 2wpb.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2WPB; Ligand: ZZI; Similar sites found: 140
This union binding pocket(no: 4) in the query (biounit: 2wpb.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4XT2 43L 0.02147 0.41043 None
2 4CLR NAP 0.01345 0.42805 1.04167
3 3BMQ NAP 0.01521 0.42646 1.04167
4 4CM4 NAP 0.01667 0.42308 1.04167
5 3JQG NAP 0.01611 0.42259 1.04167
6 4CM8 NAP 0.01717 0.4224 1.04167
7 5JDC NAP 0.01754 0.42191 1.04167
8 3JQB NAP 0.01765 0.42049 1.04167
9 3JQA NAP 0.01766 0.42047 1.04167
10 4CM9 NAP 0.02134 0.4186 1.04167
11 3JQ8 NAP 0.02156 0.41836 1.04167
12 4R6W SAH 0.04643 0.40261 1.55039
13 2BD0 NAP 0.02188 0.42033 1.63934
14 1F20 NAP 0.006211 0.42522 1.64474
15 3KLJ FAD 0.04479 0.40452 1.64474
16 2Q3O FMN 0.02976 0.4015 1.64474
17 3A25 SAM 0.01311 0.4149 1.66113
18 1PNO NAP 0.02039 0.42084 1.66667
19 5MGZ SAH 0.01781 0.40985 1.69492
20 3DJF BC3 0.01795 0.4145 1.74216
21 1RC0 KT5 0.03311 0.41375 1.91388
22 3BGD PM6 0.03506 0.4046 1.92308
23 3BGD SAH 0.02846 0.40402 1.92308
24 2H92 C5P 0.01285 0.4094 2.28311
25 2PT9 S4M 0.002974 0.45833 2.30263
26 2PT9 2MH 0.004754 0.45833 2.30263
27 4YUW S4M 0.04491 0.43969 2.30263
28 4YUW 4JU 0.04557 0.43969 2.30263
29 1RJD SAM 0.007547 0.43076 2.30263
30 5DWQ SFG 0.02953 0.4046 2.30263
31 2I7C AAT 0.004657 0.45762 2.4735
32 1BC5 SAH 0.01506 0.41848 2.60223
33 3DLS ADP 0.009595 0.41576 2.63158
34 3GDQ ADP 0.03491 0.41147 2.63158
35 3MB5 SAM 0.02154 0.41036 2.63158
36 4QYS PLP SEP 0.02791 0.4059 2.63158
37 3GL0 HXX 0.01732 0.40072 2.63158
38 1NWU NAG NAG NAG NDG 0.03501 0.4007 2.63158
39 1NFQ NAI 0.04457 0.40358 2.69231
40 3HVJ 705 0.04789 0.40684 2.71493
41 1B8O IMH 0.006369 0.44102 2.8169
42 1C3V NDP 0.04456 0.40249 2.85714
43 4C5N ACP 0.02713 0.40655 2.89855
44 1UWK NAD 0.03086 0.42433 2.96053
45 1UWK URO 0.03086 0.42433 2.96053
46 4FZV SAM 0.02826 0.40112 2.96053
47 4N49 SAM 0.01446 0.41621 3.03738
48 1G0N NDP 0.02732 0.42125 3.18021
49 1G0N PHH 0.03076 0.42111 3.18021
50 3Q9T FAY 0.01924 0.42962 3.28947
51 2P53 NNG 0.01613 0.41206 3.28947
52 5U5G NAP 0.03212 0.40786 3.38983
53 2FV5 541 0.03443 0.40743 3.44828
54 1TPY SAH 0.02555 0.40497 3.48432
55 1KPH SAH 0.03 0.40132 3.48432
56 2XVM SAH 0.01057 0.41365 3.51759
57 1KDO C 0.007678 0.42861 3.52423
58 1VE3 SAM 0.02183 0.40356 3.52423
59 3G89 SAM 0.01009 0.41467 3.61446
60 3C6K SPD 0.01531 0.43306 3.61842
61 3C6K MTA 0.01531 0.43306 3.61842
62 3JYN NDP 0.03755 0.4087 3.61842
63 2BSA NAP 0.009445 0.45708 3.63036
64 1QFY FAD 0.01422 0.4348 3.94737
65 1QFY NAP 0.01422 0.4348 3.94737
66 3G5S FAD 0.02228 0.42516 3.94737
67 4V3C C 0.01998 0.40179 3.94737
68 5HRA DAS 0.01779 0.40015 4.25532
69 3GDN HBX 0.0226 0.43575 4.27632
70 3GDN FAD 0.01737 0.43575 4.27632
71 1RRM APR 0.02671 0.40077 4.27632
72 2Q2V NAD 0.0136 0.4326 4.31373
73 1MXH DHF 0.02147 0.42701 4.34783
74 1MXH NAP 0.02746 0.42113 4.34783
75 5T67 JHZ 0.02397 0.43048 4.56731
76 5T67 SAH 0.03619 0.41631 4.56731
77 4NBT NAD 0.03993 0.40278 4.58333
78 4RJK TPP 0.02714 0.41055 4.60526
79 4RJK TDL 0.0305 0.41026 4.60526
80 4ZA2 NAD 0.04089 0.40222 4.74308
81 2UYQ SAM 0.004675 0.40197 4.83871
82 2ZWA SAH 0.006338 0.43803 4.93421
83 5IXJ THR 0.01889 0.42143 4.93421
84 4TXJ THM 0.04551 0.40087 5.06757
85 2WTX UDP 0.02967 0.41533 5.26316
86 4A2B AGS 0.01626 0.41357 5.26316
87 5EYP GTP 0.03358 0.40433 5.26316
88 4QNW FMN 0.02549 0.40345 5.26316
89 3L9R L9R 0.04167 0.40623 5.30035
90 2DTX BMA 0.04295 0.41129 5.30303
91 4LPS GDP 0.01678 0.40141 5.3719
92 3FRH SAH 0.01777 0.41473 5.5336
93 5FA8 SAM 0.02242 0.40945 5.59006
94 3CV9 VDX 0.02565 0.4131 5.59211
95 4NTC FAD 0.04671 0.41098 5.67164
96 4IF4 BEF 0.0007651 0.41032 5.76923
97 1U1F 183 0.03659 0.41939 5.85938
98 2J9D AMP 0.02228 0.4013 5.88235
99 2J9D ADP 0.03021 0.40117 5.88235
100 2J9C ATP 0.03748 0.40048 5.88235
101 1FND A2P 0.02735 0.41726 5.92105
102 1FND FAD 0.02735 0.41726 5.92105
103 4J36 1HR 0.04051 0.4161 5.92105
104 4M73 M72 0.04556 0.40804 5.92105
105 4M73 SAH 0.04572 0.40702 5.92105
106 2A8Y MTA 0.008761 0.42567 5.92593
107 4OOE FOM 0.03834 0.43508 5.94059
108 4OOE NDP 0.03834 0.43508 5.94059
109 3WGT FAD 0.03063 0.42607 6.57895
110 3WGT QSC 0.03158 0.42607 6.57895
111 5K7U SAM 0.01429 0.41299 6.57895
112 3QWI NAP 0.006186 0.451 6.66667
113 4OSP NAP 0.02687 0.41202 6.84411
114 3H4V NAP 0.03989 0.40397 6.94444
115 2CFC NAD 0.04352 0.40076 7.2
116 1X1T NAD 0.01363 0.43255 7.30769
117 5THQ NDP 0.02775 0.41247 7.35294
118 5MW4 5JU 0.0134 0.44014 7.56579
119 3QOX SAH 0.02404 0.40786 7.56579
120 3H8V ATP 0.01382 0.41373 7.87671
121 2PWY SAH 0.007803 0.43334 8.52713
122 3A27 SAM 0.009501 0.42204 8.82353
123 1I1N SAH 0.03853 0.4024 8.84956
124 2QTZ NAP 0.02115 0.42438 8.88158
125 3EYA FAD 0.04967 0.40407 9.21053
126 5LXT ACP 0.02779 0.40307 9.79021
127 1NM5 NAD 0.04674 0.4185 9.85222
128 1NM5 NAP 0.04547 0.4185 9.85222
129 3A4T SFG 0.02745 0.40484 10.9489
130 5IL1 SAM 0.01699 0.40914 11.3208
131 1EJ0 SAM 0.008017 0.4258 12.7778
132 1LSS NAD 0.01002 0.42442 12.8571
133 1AE1 NAP 0.02865 0.4151 13.9194
134 1H74 ADP 0.04895 0.40241 14.1892
135 1H74 ILE 0.04884 0.40033 14.1892
136 3NDJ SAH 0.02516 0.4301 15.7895
137 3NDJ JHZ 0.02516 0.4301 15.7895
138 1B74 DGN 0.00132 0.46217 25.9843
139 4ZOW CLM 0.01146 0.41968 31.9079
140 4PTN GXV 0.002288 0.42707 38.484
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