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Receptor
PDB id Resolution Class Description Source Keywords
1E5F 2.18 Å EC: 4.4.1.11 METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS TRICHOMONAS VAGINALIS METHIONINE BIOSYNTHESIS PLP-DEPENDENT ENZYMES C-S GAMMA LYASE LYASE
Ref.: THE STRUCTURE AND PROPOSED CATALYTIC MECHANISM OF METHIONINE GAMMA-LYASE TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:412;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PLP A:405;
B:405;
Valid;
Valid;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
SO4 A:407;
A:408;
A:409;
B:406;
B:410;
B:411;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
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
1E5F 2.18 Å EC: 4.4.1.11 METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS TRICHOMONAS VAGINALIS METHIONINE BIOSYNTHESIS PLP-DEPENDENT ENZYMES C-S GAMMA LYASE LYASE
Ref.: THE STRUCTURE AND PROPOSED CATALYTIC MECHANISM OF METHIONINE GAMMA-LYASE TO BE PUBLISHED
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1E5F - PLP C8 H10 N O6 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 3 families.
1 1E5F - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3VK3 - MET C5 H11 N O2 S CSCC[C@@H]....
2 5X2X - 4LM C12 H15 N2 O7 P C/C=C(C(=O....
3 5X2Z - 3LM C13 H19 N2 O7 P S Cc1c(c(c(c....
4 1E5F - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 4IY7 - KOU C11 H15 N2 O8 P Cc1c(c(c(c....
6 5M3Z Ki = 0.6 mM NLE C6 H13 N O2 CCCC[C@@H]....
7 4HF8 - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
8 3MKJ - PZP C8 H11 N2 O5 P [H]/N=C/c1....
9 4OMA - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
10 1CL2 - PPG C14 H20 N3 O8 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 F0G 0.564516 0.865385
12 MPM 0.564516 0.814815
13 FEV 0.555556 0.803571
14 KOU 0.555556 0.836364
15 HCP 0.546875 0.77193
16 EVM 0.546875 0.821429
17 6DF 0.545455 0.811321
18 PXL 0.541667 0.659574
19 Z98 0.537313 0.75
20 PXP 0.537037 0.862745
21 PMP 0.527273 0.767857
22 P0P 0.527273 0.916667
23 PL6 0.522388 0.818182
24 GT1 0.517857 0.830189
25 PFM 0.514706 0.803571
26 FEJ 0.514706 0.851852
27 LLP 0.5 0.737705
28 P70 0.5 0.833333
29 PUS 0.479452 0.707692
30 PL5 0.479452 0.775862
31 MPL 0.473684 0.836364
32 PLG 0.46875 0.75
33 IN5 0.46875 0.758621
34 P89 0.466667 0.714286
35 PLP PUT 0.463768 0.672131
36 EQJ 0.460526 0.725806
37 5DK 0.460526 0.725806
38 O1G 0.454545 0.75
39 PLT 0.439024 0.762712
40 X04 0.431034 0.851852
41 PDD 0.426471 0.762712
42 PP3 0.426471 0.762712
43 PDA 0.426471 0.762712
44 P1T 0.426471 0.714286
45 33P 0.42029 0.745763
46 IK2 0.42029 0.714286
47 TLP 0.414286 0.793103
48 2BK 0.414286 0.793103
49 PLS 0.414286 0.779661
50 2BO 0.414286 0.793103
51 5PA 0.414286 0.714286
52 PMH 0.414286 0.619718
53 9TD 0.413793 0.671642
54 PLP 999 0.410959 0.796296
55 PPD 0.408451 0.75
56 C6P 0.408451 0.75
57 QLP 0.405405 0.681818
58 MP5 0.403509 0.666667
59 PLA 0.402778 0.703125
60 PY5 0.402778 0.703125
61 HEY 0.4 0.703125
62 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1E5F; Ligand: PLP; Similar sites found with APoc: 149
This union binding pocket(no: 1) in the query (biounit: 1e5f.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4E3Q PMP 0.742574
2 2X5F PLP 1.23762
3 4FFG 0U8 1.23762
4 1M7Y PPG 1.48515
5 4ZM4 PLP 1.48515
6 4ZM4 P3B 1.48515
7 6DND PLP 1.73267
8 2CJH AKG 1.73267
9 2R42 FPS 1.77215
10 5TIV A3P 1.97628
11 5W19 9TD 1.9802
12 4WXG 2BO 1.9802
13 5DDW 5B6 1.9802
14 3E1T FAD 1.9802
15 1U26 IHS 2.07715
16 4ZSY RW2 2.1692
17 1AJS PLA 2.22772
18 6EWR PMP 2.22772
19 3BWN PMP 2.30179
20 3BWN PMP PHE 2.30179
21 1UU1 PMP HSA 2.38806
22 5D63 FUC GLA GLA 2.38908
23 3A8U PLP 2.47525
24 4ADC PLP 2.47525
25 3NYQ MCA 2.47525
26 3NYQ AMP 2.47525
27 1TOI HCI 2.52525
28 4JE5 PLP 2.72277
29 4JE5 PMP 2.72277
30 2R5N TPP 2.72277
31 2R5N R5P 2.72277
32 2R5N RP5 2.72277
33 1VJO PLP 2.79898
34 3WGC PLG 2.93255
35 4R5Z SIN 2.9703
36 4R5Z PMP 2.9703
37 5IWQ PLP 2.9703
38 5KGS 6SR 2.9703
39 5G09 6DF 2.9703
40 1ZC9 PMP 2.9703
41 6FYQ PLP 2.9703
42 3A23 GAL 2.9703
43 1LC8 33P 3.02198
44 1SFF IK2 3.21782
45 2HHP FLC 3.21782
46 1MLY ACZ PLP 3.21782
47 4AZJ SEP PLP 3.33333
48 5W70 9YM 3.46535
49 2OGA PGU 3.50877
50 1M32 PLP 3.55191
51 3DR4 G4M 3.58056
52 1GCK ASP PLP 3.63636
53 2R2N KYN 3.71287
54 2R2N PMP 3.71287
55 1OXO IK2 3.74065
56 4FHT DHB 3.82166
57 1DJ9 KAM 3.90625
58 5FJN BE2 3.94737
59 5FJN FAD 3.94737
60 5W71 9YM 3.9604
61 5W71 PLP 3.9604
62 4BA5 PXG 3.9604
63 4UOX PLP 3.9604
64 4ZAH T5K 4.0404
65 3HVJ 705 4.0724
66 1TDU DUR 4.15094
67 1ZPR UMP 4.16667
68 1XI9 PLP 4.20792
69 2ZYJ PGU 4.28212
70 3LN9 FLC 4.31655
71 4D57 ARG AMP 4.45545
72 3PDB PMP 4.48878
73 3PD6 PMP 4.48878
74 2HOX P1T 4.70297
75 2OAT PFM 4.70297
76 1FC4 AKB PLP 4.73815
77 2FNU PMP UD1 4.8
78 4AOA IK2 4.9505
79 3LTW HLZ 5
80 3CQ5 PMP 5.14905
81 6C3C EJ1 5.19802
82 2XBN PMP 5.44554
83 2WK9 PLG 5.65553
84 2WK9 PLP 5.65553
85 5GVL PLG 5.69307
86 5GVL GI8 5.69307
87 1O69 X04 5.69307
88 5GVR LMR 5.69307
89 5YKT PMP 5.69307
90 1LW4 PLP 5.76369
91 1LW4 TLP 5.76369
92 3EI9 PL6 5.94059
93 3QVP FAD 5.94059
94 6C92 EQJ 6.11702
95 6C8T EQJ 6.11702
96 6C9B EGV 6.11702
97 3K7S R52 6.14525
98 3QDW A2G 6.29371
99 3QDV A2G 6.29371
100 3QDX A2G GAL 6.29371
101 3QDY A2G GAL 6.29371
102 4FL0 PLP 6.43564
103 4UHO PLP 6.43564
104 1M1B SPV 6.77966
105 1MDZ PLP 6.87023
106 1MDZ DCS 6.87023
107 1KNM LAT 6.92308
108 2OFD NGA 7.04225
109 6CD1 PLS 7.42574
110 6CD1 PLG 7.42574
111 1GDE GLU PLP 7.45501
112 4LNL 2BK 7.80781
113 4LNL 2BO 7.80781
114 4LNL PLG 7.80781
115 3FQ8 PMP 7.92079
116 6CBN OZY 7.92079
117 6CBO DOW 7.97267
118 3ZRR PXG 8.07292
119 1I1D 16G 8.07453
120 3EW2 BTN 8.14815
121 3T2W BTN 8.19672
122 1DFO PLG 8.66337
123 2PO3 T4K 8.66337
124 4IRP UDP 8.76494
125 4RKC PMP 8.79397
126 5K8B PDG 8.933
127 5WYF ILP 9.15842
128 1WYV PLP AOA 9.90099
129 4K2M O1G 10.6436
130 2Z9V PXM 10.6436
131 1U08 PLP 10.8911
132 3NUB UD0 11.1421
133 3B8X G4M 11.2821
134 6ECG PM9 11.3861
135 2TPL HPP 11.3861
136 5U23 TQP 11.7801
137 1B9I PXG 11.8557
138 3VP6 HLD 12.3762
139 1C7O PPG 12.5313
140 2ZC0 PMP 13.3663
141 2X5D PLP 13.6139
142 3FRK TQP 13.6729
143 5VEQ PMP 14.3564
144 3BS8 PMP 14.3564
145 5TXR PLP 14.604
146 4M2K PLP 16.0891
147 1GEX PLP HSA 16.573
148 2R5E QLP 16.8317
149 2R5C C6P 16.8317
Pocket No.: 2; Query (leader) PDB : 1E5F; Ligand: PLP; 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: 1e5f.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1E5F; Ligand: PLP; Similar sites found with APoc: 28
This union binding pocket(no: 3) in the query (biounit: 1e5f.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5BYK A3P 1.9305
2 5BYK OAQ 1.9305
3 5CQG 55C 1.9802
4 1JS3 PLP 142 1.9802
5 1PMO PLR 1.9802
6 2HUI GLV 2.03562
7 2UUU FAD 2.22772
8 2UUU PL3 2.22772
9 5MB4 NDG 2.49377
10 5MB4 NAG 2.49377
11 1WUU ANP 2.50627
12 5WS9 OXL 2.72277
13 2RGO FAD 2.9703
14 3VMW ADA ADA ADA 3.06748
15 1NCE UMP 4.16667
16 2J0W ASP 4.70297
17 4ARE FLC 4.9505
18 4D9C PMP 5.26316
19 2PNZ UDP 5.77617
20 1T0S BML 6.97674
21 1Z17 ILE 7.26744
22 2VPY MGD 7.69231
23 3O01 DXC 9.74026
24 2R0H CTO 9.7561
25 4LHD GLY 9.90099
26 5DKK FMN 10.3448
27 2O1C PPV 16.6667
28 2YBP 2HG 41.6667
Pocket No.: 4; Query (leader) PDB : 1E5F; Ligand: PLP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1e5f.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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