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(...
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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: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 3LM 1 1
2 HEY 0.743243 0.882353
3 P1T 0.635135 0.867647
4 LPI 0.580247 0.898551
5 PLG 0.573333 0.850746
6 2BO 0.556962 0.863636
7 TLP 0.556962 0.863636
8 2BK 0.556962 0.863636
9 PDD 0.551282 0.863636
10 PP3 0.551282 0.863636
11 PDA 0.551282 0.863636
12 IK2 0.544304 0.763889
13 PLS 0.5375 0.823529
14 5PA 0.5375 0.788732
15 PLP 2KZ 0.530864 0.848485
16 PPD 0.530864 0.823529
17 C6P 0.530864 0.850746
18 ILP 0.53012 0.893939
19 PY5 0.52439 0.855072
20 PLA 0.52439 0.828571
21 IN5 0.512821 0.833333
22 PDG 0.511905 0.826087
23 CBA 0.511905 0.8
24 7XF 0.511905 0.852941
25 PGU 0.511905 0.826087
26 33P 0.506173 0.848485
27 PMG 0.505882 0.830986
28 QLP 0.505882 0.780822
29 76U 0.5 0.788732
30 PMP 0.5 0.787879
31 PY6 0.5 0.830986
32 RW2 0.494382 0.842857
33 PL4 0.494382 0.814286
34 N5F 0.494253 0.814286
35 EA5 0.494253 0.816901
36 ORX 0.494253 0.814286
37 PSZ 0.494253 0.767123
38 PE1 0.488636 0.814286
39 PL2 0.488372 0.72973
40 PXP 0.486111 0.727273
41 KAM 0.483516 0.814286
42 PMH 0.481928 0.654321
43 PXG 0.477778 0.797101
44 GT1 0.472973 0.757576
45 7TS 0.45977 0.725
46 PPG 0.456522 0.763889
47 DCS 0.454545 0.670732
48 AQ3 0.447917 0.777778
49 PL8 0.44086 0.753247
50 9YM 0.43956 0.726027
51 RMT 0.421053 0.760563
52 1D0 0.418367 0.767123
53 7B9 0.416667 0.783784
54 AN7 0.409639 0.712121
55 FOO 0.404762 0.746269
56 FEV 0.402299 0.764706
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5X2Z; Ligand: 3LM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5x2z.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5X2Z; Ligand: 3LM; 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: 5x2z.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5X2Z; Ligand: 3LM; 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: 5x2z.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5X2Z; Ligand: 3LM; 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: 5x2z.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
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