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Receptor
PDB id Resolution Class Description Source Keywords
4WXG 2 Å EC: 2.1.2.1 CRYSTAL STRUCTURE OF L-SERINE HYDROXYMETHYLTRANSFERASE IN CO A MIXTURE OF L-ALLO-THREONINE AND GLYCINE STREPTOCOCCUS THERMOPHILUS ALDOLASE TRANSFERASE ALDEHYDES CATALYSIS CATALYTIC DOMAIDIMERIZATION GLYCINE HYDROXYMETHYLTRANSFERASE L-ALLO-THREPROTEIN BINDING THREONINE ALDOLASE
Ref.: ENGINEERED L-SERINE HYDROXYMETHYLTRANSFERASE FROM STREPTOCOCCUS THERMOPHILUS FOR THE SYNTHESIS OF ALP ALPHA-DIALKYL-ALPHA-AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 3013 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2BO A:501;
C:501;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
submit data
350.262 C12 H19 N2 O8 P Cc1c(...
GOL A:503;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NA C:502;
A:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4WXG 2 Å EC: 2.1.2.1 CRYSTAL STRUCTURE OF L-SERINE HYDROXYMETHYLTRANSFERASE IN CO A MIXTURE OF L-ALLO-THREONINE AND GLYCINE STREPTOCOCCUS THERMOPHILUS ALDOLASE TRANSFERASE ALDEHYDES CATALYSIS CATALYTIC DOMAIDIMERIZATION GLYCINE HYDROXYMETHYLTRANSFERASE L-ALLO-THREPROTEIN BINDING THREONINE ALDOLASE
Ref.: ENGINEERED L-SERINE HYDROXYMETHYLTRANSFERASE FROM STREPTOCOCCUS THERMOPHILUS FOR THE SYNTHESIS OF ALP ALPHA-DIALKYL-ALPHA-AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 3013 2015
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4WXG - 2BO C12 H19 N2 O8 P Cc1c(c(c(c....
2 4WXB - CIT C6 H8 O7 C(C(=O)O)C....
3 4WXF - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2VMO - GLY PLP n/a n/a
2 2VMQ - GLY PLP n/a n/a
3 2W7F - SER PLP n/a n/a
4 2W7L - PLP ALO n/a n/a
5 1KKP - PLP SER n/a n/a
6 2VMP - SER PLP n/a n/a
7 1YJY - PLP SER n/a n/a
8 2VMW - SER PLP n/a n/a
9 2W7K - SER PLP n/a n/a
10 1KL1 - PLP GLY n/a n/a
11 2W7J - GLY PLP n/a n/a
12 2W7M - GLY PLP n/a n/a
13 2VMX - PLP ALO n/a n/a
14 1YJZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
15 2VMT - SER PLP n/a n/a
16 2W7G - PLP ALO n/a n/a
17 1YJS - PLP GLY n/a n/a
18 4WXG - 2BO C12 H19 N2 O8 P Cc1c(c(c(c....
19 4WXB - CIT C6 H8 O7 C(C(=O)O)C....
20 4WXF - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
21 1DFO - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
50% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VMO - GLY PLP n/a n/a
2 2VMQ - GLY PLP n/a n/a
3 2W7F - SER PLP n/a n/a
4 2W7L - PLP ALO n/a n/a
5 1KKP - PLP SER n/a n/a
6 2VMP - SER PLP n/a n/a
7 1YJY - PLP SER n/a n/a
8 2VMW - SER PLP n/a n/a
9 2W7K - SER PLP n/a n/a
10 1KL1 - PLP GLY n/a n/a
11 2W7J - GLY PLP n/a n/a
12 2W7M - GLY PLP n/a n/a
13 2VMX - PLP ALO n/a n/a
14 1YJZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
15 2VMT - SER PLP n/a n/a
16 2W7G - PLP ALO n/a n/a
17 1YJS - PLP GLY n/a n/a
18 4WXG - 2BO C12 H19 N2 O8 P Cc1c(c(c(c....
19 4WXB - CIT C6 H8 O7 C(C(=O)O)C....
20 4WXF - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
21 5GVN ic50 = 90 nM G6F C26 H25 F N4 O3 Cc1c2c(n[n....
22 5XMV - 8AU C24 H20 Cl F3 N4 O Cc1c2c(n[n....
23 5YFZ - 8UO C24 H28 F N5 O3 Cc1c2c(n[n....
24 5XMQ - 8A6 C32 H30 F3 N5 O3 S Cc1c2c(n[n....
25 4TN4 - 33G C25 H20 F N5 O Cc1c2c(n[n....
26 5GVL ic50 = 42 nM GI8 C24 H23 N5 O2 S Cc1c2c(n[n....
27 5XMP - 8A3 C27 H25 F6 N5 O3 S Cc1c2c(n[n....
28 5GVM ic50 = 186 nM G57 C26 H23 F3 N4 O3 Cc1c2c(n[n....
29 5XMS - 8B3 C24 H20 F4 N4 O Cc1c2c(n[n....
30 5YG4 - 8UF C25 H28 F N5 O3 Cc1c2c(n[n....
31 5XMU - 8A0 C25 H23 F3 N4 O Cc1ccccc1c....
32 5YG3 - 8UC C23 H20 F N5 O Cc1c2c(n[n....
33 5GVK Kd = 99 nM G45 C24 H24 N6 O3 S2 Cc1c2c(n[n....
34 5YG2 - N05 C25 H30 F N5 O3 Cc1c2c(n[n....
35 5GVP ic50 = 165 nM GCF C27 H25 F3 N4 O3 Cc1c2c(n[n....
36 5V7I - GLY C2 H5 N O2 C(C(=O)O)N
37 1DFO - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2BO; Similar ligands found: 73
No: Ligand ECFP6 Tc MDL keys Tc
1 2BK 1 1
2 2BO 1 1
3 TLP 1 1
4 ILP 0.791045 0.934426
5 PDD 0.753846 0.966102
6 PDA 0.753846 0.966102
7 PP3 0.753846 0.966102
8 PLS 0.705882 0.95
9 PPD 0.695652 0.918033
10 C6P 0.695652 0.918033
11 PY5 0.685714 0.890625
12 IN5 0.681818 0.932203
13 7XF 0.666667 0.888889
14 PDG 0.666667 0.888889
15 PGU 0.666667 0.888889
16 ORX 0.662162 0.875
17 N5F 0.662162 0.875
18 LPI 0.657534 0.850746
19 QLP 0.657534 0.835821
20 PE1 0.653333 0.875
21 PY6 0.648649 0.863636
22 PLG 0.632353 0.918033
23 76U 0.626667 0.846154
24 CBA 0.621622 0.919355
25 33P 0.619718 0.885246
26 PL4 0.615385 0.875
27 P1T 0.605634 0.875
28 KAM 0.6 0.875
29 IK2 0.597222 0.846154
30 5PA 0.589041 0.875
31 EA5 0.576923 0.848485
32 PLA 0.573333 0.890625
33 AQ3 0.571429 0.861538
34 HEY 0.564103 0.861538
35 3LM 0.556962 0.863636
36 PMP 0.553846 0.881356
37 PMG 0.551282 0.863636
38 GT1 0.545455 0.786885
39 PXP 0.538462 0.844828
40 PSZ 0.5375 0.820895
41 PMH 0.526316 0.739726
42 RW2 0.518072 0.820895
43 PXG 0.518072 0.887097
44 PL2 0.5125 0.753623
45 DCS 0.5125 0.756757
46 7TS 0.5 0.746667
47 9YM 0.47619 0.830769
48 PLP 2KZ 0.4625 0.854839
49 F0G 0.461538 0.816667
50 PL8 0.45977 0.753425
51 PLR 0.454545 0.745763
52 7B9 0.449438 0.785714
53 FEJ 0.445783 0.836066
54 PPG 0.443182 0.818182
55 P0P 0.442857 0.793103
56 KOU 0.4375 0.852459
57 0JO 0.43038 0.738462
58 RMT 0.422222 0.787879
59 PLP 2TL 0.421687 0.933333
60 CAN PLP 0.420455 0.794118
61 PUS 0.420455 0.708333
62 1D0 0.419355 0.848485
63 PL6 0.416667 0.75
64 EVM 0.414634 0.83871
65 PLP 0.414286 0.793103
66 4LM 0.4125 0.777778
67 Z98 0.411765 0.8
68 AN7 0.410256 0.766667
69 EPC 0.410256 0.783333
70 PZP 0.408451 0.766667
71 LCS 0.406977 0.697368
72 FOO 0.405063 0.803279
73 FEV 0.402439 0.765625
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4WXG; Ligand: 2BO; Similar sites found with APoc: 164
This union binding pocket(no: 1) in the query (biounit: 4wxg.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZC0 PMP 1.7199
2 5WYF ILP 1.86916
3 5YKT PMP 1.86916
4 1K4M CIT 1.87793
5 4M2K PLP 1.97044
6 1E5F PLP 1.9802
7 2HW1 FRU 2.01342
8 1U26 IHS 2.07715
9 2X5F PLP 2.1028
10 1JS3 PLP 142 2.1028
11 1ZC9 PMP 2.1028
12 3CQ5 PMP 2.16802
13 6C3C EJ1 2.17918
14 1LC8 33P 2.1978
15 3PDB PMP 2.24439
16 3PD6 PMP 2.24439
17 4E1O PLP PVH 2.33645
18 3FQ8 PMP 2.34192
19 1SFF IK2 2.34742
20 6DND PLP 2.43309
21 3ZDS HQ9 2.57009
22 4ZSY RW2 2.57009
23 4JE5 PLP 2.57009
24 4JE5 PMP 2.57009
25 3ZDS OMD 2.57009
26 1OXO IK2 2.74314
27 3BS8 PMP 2.80374
28 1QMG DMV 2.80374
29 2VAR KDG 2.8754
30 2VAR KDF 2.8754
31 5U23 TQP 2.87958
32 5K8B PDG 2.97767
33 1DJ9 KAM 3.03738
34 5IWQ PLP 3.03738
35 2X5D PLP 3.15534
36 2OMN IPH 3.22581
37 2B6N ALA PRO THR 3.23741
38 4RKC PMP 3.26633
39 5DDW 5B6 3.27103
40 6A4R ASP 3.27103
41 3QTP 2PG 3.27103
42 1M32 PLP 3.27869
43 1VJO PLP 3.30789
44 4R8L ASP 3.37662
45 3ZRR PXG 3.38542
46 5LUB 3Y7 3.43511
47 1KGZ PRP 3.47826
48 1PMO PLR 3.50467
49 1M7Y PPG 3.50467
50 2B4B B33 3.50877
51 6DXS HJ7 3.50877
52 4IY7 KOU 3.52645
53 4IY7 0JO 3.52645
54 4IYO 0JO 3.52645
55 1TOI HCI 3.53535
56 4L9Z OXL 3.53982
57 1CL2 PPG 3.5443
58 1UU1 PMP HSA 3.58209
59 1U08 PLP 3.62694
60 1GCK ASP PLP 3.63636
61 3WYW GSH 3.7037
62 1F6D UDP 3.7234
63 2FNU PMP UD1 3.73333
64 5W71 9YM 3.73832
65 4ZM4 PLP 3.73832
66 5W71 PLP 3.73832
67 4ZM4 P3B 3.73832
68 2FYF PLP 3.76884
69 5U83 ZN8 3.77358
70 5BOE PEP 3.97196
71 5CSS G3P 3.9823
72 6H45 QEI 4.08163
73 4ADC PLP 4.18719
74 4M3P HCS 4.18719
75 4UOX PLP 4.20561
76 4UHO PLP 4.20561
77 4UOX PUT 4.20561
78 2UZH IPE 4.24242
79 4ZAH T5K 4.29293
80 5G09 6DF 4.34783
81 2R2N PMP 4.47059
82 1O69 X04 4.56853
83 2OAT PFM 4.6729
84 6CBO DOW 4.6729
85 1ELU PDA 4.87179
86 1ELU CSS 4.87179
87 4A59 AMP 4.90654
88 4AOA IK2 4.90654
89 5X30 7XF 5.02513
90 5X30 4LM 5.02513
91 5X2Z 3LM 5.02513
92 6C8T EQJ 5.05319
93 6C9B EGV 5.05319
94 6C92 EQJ 5.05319
95 5VEQ PMP 5.10949
96 3A8U PLP 5.14019
97 4B98 PXG 5.14019
98 4YDD MGD 5.14019
99 4YDD MD1 5.14019
100 2OGA PGU 5.26316
101 4R5Z PMP 5.44959
102 4R5Z SIN 5.44959
103 2R5E QLP 5.59441
104 2R5C C6P 5.59441
105 6FYQ PLP 5.60748
106 4E3Q PMP 5.60748
107 1WYV PLP AOA 5.84112
108 2HHP FLC 6.07477
109 4HVK PMP 6.30841
110 5G4J EXT 6.30841
111 2C1P FNZ 6.45161
112 4FL0 PLP 6.54206
113 1V1A KDG 6.54206
114 6CZY PMP 6.62983
115 5W19 9TD 6.7757
116 4AZJ SEP PLP 6.94444
117 2JG1 TA6 6.9697
118 4OSP 2V4 7.22433
119 5M60 BGC 7.24299
120 2HOX P1T 7.47664
121 3BWN PMP 7.67263
122 1FDJ 13P 7.98898
123 2TPL HPP 8.17757
124 5V3D FCN 8.27586
125 1LW4 TLP 8.93372
126 1LW4 PLP 8.93372
127 3VWX GSH 9.00901
128 1O8B ABF 9.13242
129 6ECG PM9 9.34579
130 3VP6 HLD 9.57944
131 1B9I PXG 9.81308
132 1AJS PLA 9.95146
133 5VYQ TYD 10.1961
134 1WB4 SXX 10.4377
135 4K2M O1G 10.7477
136 3WGC PLG 11.4369
137 1MLY ACZ PLP 11.655
138 1FC4 AKB PLP 11.6822
139 5KGS 6SR 11.9159
140 4BA5 PXG 12.4183
141 1MDZ PLP 13.7405
142 1MDZ DCS 13.7405
143 3DR4 G4M 13.8107
144 2EB5 OXL 14.2322
145 2WK9 PLG 14.2523
146 2WK9 PLP 14.2523
147 3FRK TQP 14.7453
148 2XBN PMP 15.2225
149 2Z9V PXM 16.1215
150 2Y91 98J 16.2264
151 1GEX PLP HSA 16.573
152 5W70 9YM 17.0561
153 6EWR PMP 17.9907
154 2PO3 T4K 18.3962
155 5TXR PLP 18.9252
156 4LNL 2BO 19.2192
157 4LNL 2BK 19.2192
158 4LNL PLG 19.2192
159 3B8X G4M 19.2308
160 3NUB UD0 20.6128
161 5M3Z NLE 23.8318
162 5M3Z PLP 23.8318
163 5M3Z PY6 23.8318
164 4BXF AKG 47.3684
Pocket No.: 2; Query (leader) PDB : 4WXG; Ligand: 2BO; Similar sites found with APoc: 17
This union binding pocket(no: 2) in the query (biounit: 4wxg.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1GQY ACP 1.40187
2 2BHZ MAL 1.63551
3 1DLL LAT 1.86916
4 5EO8 TFU 2.2508
5 3EQO LGC 2.5066
6 5EOO CIT 3.01887
7 4UOZ GLA 3.73832
8 3FC4 EDO 3.97196
9 2P1E LAC 4.82315
10 5FII PHE 6.86275
11 1II5 GLU 6.86695
12 3TUR DGL 7.31707
13 3KJQ B94 7.36842
14 3BWN PMP PHE 7.67263
15 5GSN MMZ 8.83002
16 2FLI DX5 10
17 2WT9 NIO 12.766
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