Receptor
PDB id Resolution Class Description Source Keywords
5X2Z 1.8 Å EC: 4.4.1.11 CRYSTAL STRUCTURE OF PSEUDOMONAS PUTIDA METHIONINE GAMMA-LYA MUTANT WITH L-METHIONINE INTERMEDIATES PSEUDOMONAS PUTIDA PYRIDOXAL 5-prime -PHOSPHATE LYASE
Ref.: STRUCTURAL AND MECHANISTIC INSIGHTS INTO HOMOCYSTEI DEGRADATION BY A MUTANT OF METHIONINE GAMMA-LYASE B SUBSTRATE-ASSISTED CATALYSIS PROTEIN SCI. V. 26 1224 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3LM C:401;
D:401;
A:401;
B:401;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
378.338 C13 H19 N2 O7 P S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5X2Z 1.8 Å EC: 4.4.1.11 CRYSTAL STRUCTURE OF PSEUDOMONAS PUTIDA METHIONINE GAMMA-LYA MUTANT WITH L-METHIONINE INTERMEDIATES PSEUDOMONAS PUTIDA PYRIDOXAL 5-prime -PHOSPHATE LYASE
Ref.: STRUCTURAL AND MECHANISTIC INSIGHTS INTO HOMOCYSTEI DEGRADATION BY A MUTANT OF METHIONINE GAMMA-LYASE B SUBSTRATE-ASSISTED CATALYSIS PROTEIN SCI. V. 26 1224 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 5M3Z Ki = 0.6 mM NLE C6 H13 N O2 CCCC[C@@H]....
5 4HF8 - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
6 3MKJ - PZP C8 H11 N2 O5 P [H]/N=C/c1....
7 4OMA - LCS C11 H14 N3 O7 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: 3LM; Similar ligands found: 54
No: Ligand ECFP6 Tc MDL keys Tc
1 3LM 1 1
2 HEY 0.743243 0.882353
3 P1T 0.635135 0.867647
4 PLG 0.573333 0.850746
5 2BO 0.556962 0.863636
6 TLP 0.556962 0.863636
7 2BK 0.556962 0.863636
8 PDD 0.551282 0.863636
9 PP3 0.551282 0.863636
10 PDA 0.551282 0.863636
11 IK2 0.544304 0.763889
12 5PA 0.5375 0.788732
13 PLS 0.5375 0.823529
14 C6P 0.530864 0.850746
15 PLP 2KZ 0.530864 0.848485
16 PPD 0.530864 0.823529
17 ILP 0.53012 0.893939
18 PY5 0.52439 0.855072
19 PLA 0.52439 0.828571
20 IN5 0.512821 0.833333
21 PDG 0.511905 0.826087
22 PGU 0.511905 0.826087
23 7XF 0.511905 0.852941
24 CBA 0.511905 0.8
25 33P 0.506173 0.848485
26 QLP 0.505882 0.780822
27 PMG 0.505882 0.830986
28 PY6 0.5 0.830986
29 PMP 0.5 0.787879
30 76U 0.5 0.788732
31 PL4 0.494382 0.814286
32 RW2 0.494382 0.842857
33 PSZ 0.494253 0.767123
34 ORX 0.494253 0.814286
35 N5F 0.494253 0.814286
36 EA5 0.494253 0.816901
37 PE1 0.488636 0.814286
38 PL2 0.488372 0.72973
39 PXP 0.486111 0.727273
40 KAM 0.483516 0.814286
41 PMH 0.481928 0.654321
42 PXG 0.477778 0.797101
43 GT1 0.472973 0.757576
44 7TS 0.45977 0.725
45 PPG 0.456522 0.763889
46 DCS 0.454545 0.670732
47 AQ3 0.447917 0.777778
48 PL8 0.44086 0.753247
49 9YM 0.43956 0.726027
50 1D0 0.418367 0.767123
51 7B9 0.416667 0.783784
52 PLP ALO 0.413793 0.820895
53 AN7 0.409639 0.712121
54 FOO 0.404762 0.746269
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5X2Z; Ligand: 3LM; Similar sites found: 86
This union binding pocket(no: 1) in the query (biounit: 5x2z.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RKC PMP 0.001195 0.45752 1.25628
2 2WCI GSH 0.03402 0.4023 1.48148
3 1AJS PLA 0.0003951 0.44914 1.50754
4 5CQG 55C 0.003081 0.45502 1.75879
5 4UOX PLP 0.00222 0.44938 1.75879
6 4AOA IK2 0.003885 0.42917 2.01005
7 3BWN PMP 0.00009047 0.51673 2.04604
8 3BWN PMP PHE 0.0007341 0.44558 2.04604
9 4E3Q PMP 0.002705 0.44998 2.26131
10 4ZM4 PLP 0.002621 0.44136 2.26131
11 1C7O PPG 0.00303 0.42278 2.26131
12 4ZSY RW2 0.00319 0.41838 2.26131
13 2HHP FLC 0.03525 0.41298 2.26131
14 3X01 AMP 0.03054 0.40711 2.29008
15 4B98 PXG 0.000754 0.45758 2.51256
16 4UHO PLP 0.01693 0.41874 2.51256
17 5DDW 5B6 0.004323 0.41274 2.51256
18 1M32 PLP 0.03752 0.40028 2.73224
19 5WYF ILP 0.003137 0.42213 2.76382
20 2Z49 AMG 0.03948 0.40072 2.76382
21 5U23 TQP 0.0009359 0.40477 2.87958
22 3OPT AKG 0.03167 0.40493 2.94906
23 5GVR LMR 0.03038 0.41625 2.99145
24 3B1E P1T 0.0008961 0.46345 3.06122
25 4ADC PLP 0.003237 0.44143 3.26633
26 2X5F PLP 0.0006345 0.48125 3.51759
27 5G09 6DF 0.0003141 0.46559 3.51759
28 4JE5 PLP 0.01026 0.42117 3.76884
29 4JE5 PMP 0.01184 0.41806 3.76884
30 5DO8 BGC 0.01788 0.41749 3.76884
31 4OKD GLC GLC GLC 0.04122 0.40068 3.76884
32 2X5D PLP 0.00158 0.47386 4.0201
33 3VMW ADA ADA ADA 0.04019 0.40055 4.29448
34 1MLY ACZ PLP 0.002667 0.42886 4.52261
35 3VP6 HLD 0.004797 0.40176 4.52261
36 5W3Y ACO 0.01085 0.42459 4.54545
37 1ZC9 PMP 0.0005942 0.45781 5.02513
38 4WXG 2BO 0.0008827 0.43483 5.02513
39 5DJ3 5DK 0.0005555 0.45911 5.05319
40 2CFC KPC 0.03706 0.40209 5.2
41 4BA5 PXG 0.0006669 0.46463 5.27638
42 3C8F MT2 0.008889 0.42959 5.71429
43 2R5E QLP 0.0001065 0.48601 6.03015
44 2R5C C6P 0.0001111 0.48521 6.03015
45 3PD6 PMP 0.0007993 0.47627 6.03015
46 3PDB PMP 0.001011 0.46593 6.03015
47 3EI9 PL6 0.001044 0.43184 6.03015
48 1GDE GLU PLP 0.0006819 0.45515 6.16967
49 5IWQ PLP 0.001035 0.46544 6.28141
50 2ZYJ PGU 0.002765 0.40465 6.29723
51 4FL0 PLP 0.0008905 0.46861 7.28643
52 5K8B PDG 0.0003919 0.45316 7.53769
53 1WYV PLP AOA 0.004116 0.42415 7.78894
54 1SFF IK2 0.004516 0.41524 7.78894
55 5W70 9YM 0.000141 0.48071 8.0402
56 1DJ9 KAM 0.00005102 0.51632 8.59375
57 4R5Z PMP 0.000396 0.45297 8.99183
58 4R5Z SIN 0.0003117 0.43699 8.99183
59 1ELU PDA 0.003949 0.42129 9.48718
60 5W71 9YM 0.003956 0.41964 10.3015
61 5W71 PLP 0.0003937 0.4138 10.3015
62 1XI9 PLP 0.0005668 0.48961 10.5528
63 3CQ5 PMP 0.00007977 0.5404 10.8401
64 4ZAH T5K 0.000552 0.42626 10.8586
65 4AG9 16G 0.01709 0.41009 10.9091
66 1DFO PLG 0.0006283 0.41352 11.3065
67 2HOX P1T 0.00008077 0.49626 11.809
68 2ZC0 PMP 0.000522 0.46482 12.0603
69 1U08 PLP 0.00002373 0.55207 12.1762
70 1Z17 ILE 0.02149 0.41523 12.5
71 1UU1 PMP HSA 0.0002029 0.46938 12.5373
72 3E2Y PMP 0.0000257 0.54321 12.8141
73 3B8X G4M 0.0003632 0.40542 12.8205
74 3FRK TQP 0.00122 0.4004 13.1367
75 1GCK ASP PLP 0.0002273 0.4717 14.2857
76 4K2M O1G 0.001582 0.42783 15.0754
77 2WK9 PLG 0.000007726 0.46858 15.6812
78 2WK9 PLP 0.00003175 0.45794 15.6812
79 2R2N PMP 0.0009021 0.46833 17.0854
80 2OGA PGU 0.001452 0.43296 20.603
81 2IDO TMP 0.03996 0.40077 22.8916
82 1FC4 AKB PLP 0.0005617 0.45889 23.3668
83 1LW4 TLP 0.001197 0.40045 30.2594
84 2Q8E OGA 0.03239 0.40478 31.25
85 3WGC PLG 0.0005471 0.46862 32.8446
86 2YBP 2HG 0.03201 0.4051 41.6667
Pocket No.: 2; Query (leader) PDB : 5X2Z; Ligand: 3LM; 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: 5x2z.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5X2Z; Ligand: 3LM; 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: 5x2z.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5X2Z; Ligand: 3LM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5x2z.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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