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Receptor
PDB id Resolution Class Description Source Keywords
4E3Q 1.9 Å EC: 2.-.-.- PMP-BOUND FORM OF AMINOTRANSFERASE CRYSTAL STRUCTURE FROM VI FLUVIALIS VIBRIO FLUVIALIS AMINOTRANSFERASE TRANSFERASE
Ref.: REDESIGNING AND CHARACTERIZING THE SUBSTRATE SPECIF ACTIVITY OF VIBRIO FLUVIALIS AMINOTRANSFERASE FOR T SYNTHESIS OF IMAGABALIN. PROTEIN ENG.DES.SEL. V. 26 25 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BEN A:503;
A:504;
B:502;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
120.152 C7 H8 N2 [H]/N...
NA A:501;
B:501;
C:501;
D:501;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
PMP A:505;
B:503;
C:503;
D:502;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
248.173 C8 H13 N2 O5 P Cc1c(...
SO4 A:502;
C:502;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4E3Q 1.9 Å EC: 2.-.-.- PMP-BOUND FORM OF AMINOTRANSFERASE CRYSTAL STRUCTURE FROM VI FLUVIALIS VIBRIO FLUVIALIS AMINOTRANSFERASE TRANSFERASE
Ref.: REDESIGNING AND CHARACTERIZING THE SUBSTRATE SPECIF ACTIVITY OF VIBRIO FLUVIALIS AMINOTRANSFERASE FOR T SYNTHESIS OF IMAGABALIN. PROTEIN ENG.DES.SEL. V. 26 25 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 4E3Q - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 4E3Q - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 4E3Q - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PMP; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 PMP 1 1
2 PXP 0.7 0.888889
3 GT1 0.673077 0.793103
4 PLG 0.57377 0.866667
5 IN5 0.57377 0.912281
6 P1T 0.571429 0.825397
7 PLR 0.557692 0.781818
8 2BK 0.553846 0.881356
9 2BO 0.553846 0.881356
10 TLP 0.553846 0.881356
11 PDD 0.546875 0.881356
12 PP3 0.546875 0.881356
13 PDA 0.546875 0.881356
14 ILP 0.544118 0.852459
15 IK2 0.538462 0.825397
16 33P 0.538462 0.896552
17 PMH 0.530303 0.742857
18 5PA 0.530303 0.825397
19 PLS 0.530303 0.866667
20 PLP 0.527273 0.767857
21 PPD 0.522388 0.866667
22 C6P 0.522388 0.866667
23 ORX 0.521127 0.854839
24 PXM 0.52 0.735849
25 PZP 0.517857 0.836364
26 PLA 0.514706 0.8125
27 PY5 0.514706 0.8125
28 PL2 0.514286 0.84127
29 QLP 0.514286 0.815385
30 PE1 0.513889 0.854839
31 PPG 0.513514 0.825397
32 P0P 0.508772 0.8
33 HEY 0.507042 0.8125
34 PDG 0.5 0.83871
35 CBA 0.5 0.83871
36 EA5 0.5 0.828125
37 3LM 0.5 0.787879
38 7XF 0.5 0.83871
39 7TS 0.5 0.702703
40 PGU 0.5 0.83871
41 9YM 0.493151 0.868852
42 DCS 0.492958 0.712329
43 PMG 0.492958 0.787879
44 LPI 0.492958 0.776119
45 LCS 0.492958 0.675676
46 76U 0.486111 0.825397
47 PY6 0.486111 0.787879
48 PL4 0.48 0.854839
49 PSZ 0.479452 0.8
50 N5F 0.479452 0.825397
51 0JO 0.462687 0.714286
52 4LM 0.462687 0.725806
53 AN7 0.461538 0.741379
54 PXG 0.460526 0.866667
55 RW2 0.460526 0.8
56 FOO 0.454545 0.75
57 PL8 0.454545 0.732394
58 NPL 0.45 0.898305
59 FEV 0.449275 0.714286
60 KAM 0.448718 0.825397
61 RMT 0.448718 0.765625
62 1D0 0.444444 0.8
63 2B1 0.443038 0.690141
64 7B9 0.443038 0.764706
65 P3D 0.442857 0.85
66 EVM 0.442857 0.786885
67 EPC 0.439394 0.789474
68 MP5 0.438596 0.728814
69 PLP CYS 0.43662 0.836066
70 EXT 0.432836 0.79661
71 AQ3 0.426829 0.8125
72 2B6 0.426829 0.662162
73 MPM 0.414286 0.75
74 F0G 0.414286 0.762712
75 PLP 2TL 0.410959 0.85
76 KOU 0.408451 0.8
77 PLP SEP 0.405405 0.85
78 PLP BH2 0.405405 0.85
79 SEP PLP 0.405405 0.85
80 HCP 0.402778 0.741935
81 LEU PLP 0.4 0.822581
82 Z98 0.4 0.777778
83 PFM 0.4 0.770492
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4E3Q; Ligand: PMP; Similar sites found with APoc: 177
This union binding pocket(no: 1) in the query (biounit: 4e3q.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1E5F PLP 0.742574
2 4ZKD GDP 0.845666
3 4AZJ SEP PLP 1.38889
4 1QPB PYM 1.47992
5 1QPB TPP 1.47992
6 3CQ5 PMP 1.62602
7 1PG4 PRX 1.69133
8 1PG4 COA 1.69133
9 4RKC PMP 1.75879
10 2GJN FMN 1.82927
11 2GJN NIS 1.82927
12 2R5C C6P 1.8648
13 2R5E QLP 1.8648
14 3VP6 HLD 1.90275
15 1NB9 ADP 2.04082
16 1NB9 RBF 2.04082
17 2HOX P1T 2.10773
18 4MIG G3F 2.11416
19 1R27 MGD 2.11416
20 1GEX PLP HSA 2.24719
21 5X2Z 3LM 2.26131
22 5X30 7XF 2.26131
23 5X30 4LM 2.26131
24 2ZYJ PGU 2.267
25 4IY7 KOU 2.267
26 4IY7 0JO 2.267
27 4IYO 0JO 2.267
28 1LW4 TLP 2.30548
29 1LW4 PLP 2.30548
30 3EI9 PL6 2.31481
31 2D1S SLU 2.32558
32 6C8T EQJ 2.39362
33 6C92 EQJ 2.39362
34 6C9B EGV 2.39362
35 4WGF HX2 2.43902
36 6CD1 PLG 2.63736
37 6CD1 PLS 2.63736
38 1WB4 SXX 2.6936
39 4K2M O1G 2.7088
40 3GP3 SEP 2.72374
41 4PVV HO4 2.77778
42 5W19 9TD 2.78373
43 4Q4K FMN 2.80112
44 3PD6 PMP 2.99252
45 3PDB PMP 2.99252
46 1M32 PLP 3.00546
47 1H74 ADP 3.04054
48 2TPL HPP 3.07018
49 6ECG PM9 3.07692
50 6CBN OZY 3.19635
51 1PMO PLR 3.21888
52 5M3Z PLP 3.26633
53 5M3Z NLE 3.26633
54 5M3Z PY6 3.26633
55 1K4M CIT 3.28639
56 4IJ6 SEP 3.31754
57 1B9I PXG 3.35052
58 4LNL PLG 3.38266
59 4LNL 2BK 3.38266
60 4LNL 2BO 3.38266
61 1TX4 ALF GDP 3.38983
62 1JG3 ADN 3.40426
63 1MJT NAD 3.59408
64 4E1O PLP PVH 3.59408
65 1GPE FAD 3.59408
66 5NWD 9C8 3.66492
67 4NCN GTP 3.71991
68 2XBN PMP 3.74707
69 3TLJ SAH 3.75335
70 5TXR PLP 3.8055
71 1OXO IK2 3.8055
72 1JS3 PLP 142 3.8055
73 1ZPD DPX 3.8055
74 1VJO PLP 3.81679
75 5IFK HPA 3.84615
76 4M73 M72 3.85757
77 4M73 SAH 3.85757
78 1GS5 ANP 3.87597
79 1GS5 NLG 3.87597
80 3ZRR PXG 3.90625
81 3DAA PDD 3.97112
82 3BF1 ADP 4.01606
83 3BF1 PAU 4.01606
84 2VBF TPP 4.01691
85 2C5L GTP 4.04624
86 1GCK ASP PLP 4.15584
87 4YNU FAD 4.22833
88 3FRK TQP 4.28954
89 3B8X G4M 4.35897
90 1U08 PLP 4.40415
91 2PO3 T4K 4.48113
92 2FYF PLP 4.52261
93 3Q9T FAY 4.65116
94 1UU1 PMP HSA 4.77612
95 4ZAH T5K 4.79798
96 4C3Y FAD 4.86258
97 4TMZ GSP 4.92754
98 1LC8 33P 4.94506
99 1DJ9 KAM 4.94792
100 1M7Y PPG 5.05747
101 3C1M ANP 5.074
102 5A89 ADP 5.12821
103 5A89 FMN 5.12821
104 1DMH MCT 5.14469
105 2R2N KYN 5.17647
106 2R2N PMP 5.17647
107 2J5V PCA 5.17711
108 1TOI HCI 5.30303
109 5W71 9YM 5.45455
110 5W71 PLP 5.45455
111 5IWQ PLP 5.52995
112 4RD0 GDP 5.54217
113 6C3C EJ1 5.56901
114 3WGC PLG 5.57185
115 4WXG 2BO 5.60748
116 2ZC0 PMP 5.65111
117 1WA5 GTP 5.70825
118 3THR C2F 5.80205
119 6EWR PMP 5.8548
120 1O94 ADP 6.13108
121 5BSH PRO 6.13718
122 5HGZ MLA 6.17284
123 4D9C PMP 6.43275
124 5W70 9YM 6.51685
125 5VEQ PMP 6.56934
126 4M0R 644 6.59631
127 1WYV PLP AOA 6.76533
128 4HVK PMP 6.80628
129 3DR4 G4M 6.90537
130 2F9W PAU 7.01107
131 1AJS PLA 7.28155
132 6DND PLP 7.29927
133 3FPZ AHZ 7.36196
134 2Z9V PXM 7.39796
135 1FC4 AKB PLP 7.4813
136 3LA3 2FT 7.81893
137 6CZY PMP 8.01105
138 3WXM GTP 8.2774
139 3GDH SAH 8.29876
140 1R18 SAH 8.37004
141 1DFO PLG 8.39329
142 2CCV A2G 8.91089
143 1NV8 MEQ 9.15493
144 1NV8 SAM 9.15493
145 5K8B PDG 9.42928
146 2JFV FLC 9.62199
147 1GUA GNP 10.1796
148 3X1Z GNP 10.1796
149 4HDO GNP 10.1796
150 2WK9 PLP 10.2828
151 2WK9 PLG 10.2828
152 2YLN CYS 10.9541
153 1K1Y MAL 11.2051
154 2J0W ADP 13.363
155 4BNU 9KQ 14.8699
156 5YKT PMP 21.2581
157 4ZSY RW2 25.1627
158 3FQ8 PMP 31.6159
159 5DDW 5B6 33.4038
160 4UOX PLP 35.3319
161 4UOX PUT 35.3319
162 4UOX PLP PUT 35.3319
163 2CJH AKG 35.412
164 3BS8 PMP 39.2694
165 2OAT PFM 42.1412
166 5G4J EXT 42.1525
167 5KGS 6SR 42.2319
168 1MLY ACZ PLP 42.4242
169 5G09 6DF 42.4947
170 5WYF ILP 42.6407
171 1ZC9 PMP 42.9561
172 1SFF IK2 43.4272
173 4B98 PXG 43.5268
174 4ADC PLP 45.0739
175 4UHO PLP 45.9402
176 3A8U PLP 46.9933
177 6FYQ PLP 49.4715
Pocket No.: 2; Query (leader) PDB : 4E3Q; Ligand: PMP; Similar sites found with APoc: 29
This union binding pocket(no: 2) in the query (biounit: 4e3q.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1FEC FAD 1.05708
2 4CE5 PDG 2.1021
3 2E5V FAD 2.33051
4 4NTD FAD 2.35294
5 4JE5 PMP 2.537
6 4JE5 PLP 2.537
7 3PNL ADP 2.8436
8 4MZU COA 2.88462
9 2UVO NAG 2.92398
10 6BKA FMN 2.94118
11 2IW1 U2F 3.20856
12 2HHP FLC 3.59408
13 5ZYN FAD 3.60934
14 1CL2 PPG 3.79747
15 2YI0 YI0 3.93013
16 4FL0 PLP 3.94737
17 2GRU NAD 4.07609
18 3TKL GTP 4.59184
19 4R5Z SIN 4.90463
20 4R5Z PMP 4.90463
21 3MGB PAP 5.95611
22 4UTG ANP 6.06936
23 6GAS FAD 6.13108
24 4P5E N6P 6.57895
25 1T0S BML 6.9697
26 1ELU PDA 7.39958
27 5M3E APR 7.87879
28 1LFD GNP 8.38323
29 1U1I NAD 11.7347
Pocket No.: 3; Query (leader) PDB : 4E3Q; Ligand: PMP; 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: 4e3q.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4E3Q; Ligand: PMP; Similar sites found with APoc: 8
This union binding pocket(no: 4) in the query (biounit: 4e3q.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3B1Q NOS 1.22699
2 4UUW AMP 3.29949
3 6F7L FAD 3.39367
4 2I3G NAP 3.40909
5 1IBR GNP 4.62963
6 1IYE PGU 5.17799
7 2VWA PTY 6.93069
8 3VMF GTP 8.40909
Pocket No.: 5; Query (leader) PDB : 4E3Q; Ligand: PMP; 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: 4e3q.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4E3Q; Ligand: PMP; Similar sites found with APoc: 18
This union binding pocket(no: 6) in the query (biounit: 4e3q.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4RSL FAD 1.34831
2 3EYA FAD 1.47992
3 5AA4 6X4 1.99557
4 2RAB FAD 2.37581
5 1DL5 SAH 2.52366
6 1U26 IHS 2.96736
7 2Q4W FAD 3.17125
8 4Y9J FAD 3.17125
9 4YSX FAD 3.20513
10 1YZN GNP 3.24324
11 1KMQ GNP 3.26087
12 3FC4 EDO 3.38266
13 5AHM IMP 4.75
14 1Q0S SAH 5.79151
15 1NAA 6FA 6.76533
16 1VG8 GNP 9.17874
17 1JQY A32 11.6505
18 1NF3 GNP 16.4062
Pocket No.: 7; Query (leader) PDB : 4E3Q; Ligand: PMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 4e3q.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 4E3Q; Ligand: PMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4e3q.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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