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 (11)
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 6NBA - P1T C11 H15 N2 O7 P Cc1c(c(c(c....
6 4IY7 - KOU C11 H15 N2 O8 P Cc1c(c(c(c....
7 5M3Z Ki = 0.6 mM NLE C6 H13 N O2 CCCC[C@@H]....
8 4HF8 - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
9 3MKJ - PZP C8 H11 N2 O5 P [H]/N=C/c1....
10 4OMA - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
11 1CL2 - PPG C14 H20 N3 O8 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3LM; Similar ligands found: 58
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 2BK 0.556962 0.863636
7 TLP 0.556962 0.863636
8 2BO 0.556962 0.863636
9 PDA 0.551282 0.863636
10 PP3 0.551282 0.863636
11 PDD 0.551282 0.863636
12 IK2 0.544304 0.763889
13 5PA 0.5375 0.788732
14 PLS 0.5375 0.823529
15 C6P 0.530864 0.850746
16 PPD 0.530864 0.823529
17 PLP 2KZ 0.530864 0.848485
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 PGU 0.511905 0.826087
23 CBA 0.511905 0.8
24 7XF 0.511905 0.852941
25 PDG 0.511905 0.826087
26 33P 0.506173 0.848485
27 CKT 0.506173 0.808824
28 PMG 0.505882 0.830986
29 QLP 0.505882 0.780822
30 PY6 0.5 0.830986
31 PMP 0.5 0.787879
32 76U 0.5 0.788732
33 PL4 0.494382 0.814286
34 RW2 0.494382 0.842857
35 ORX 0.494253 0.814286
36 N5F 0.494253 0.814286
37 EA5 0.494253 0.816901
38 PSZ 0.494253 0.767123
39 PE1 0.488636 0.814286
40 PL2 0.488372 0.72973
41 PXP 0.486111 0.727273
42 KAM 0.483516 0.814286
43 PMH 0.481928 0.654321
44 DN9 0.478261 0.763158
45 PXG 0.477778 0.797101
46 GT1 0.472973 0.757576
47 7TS 0.45977 0.725
48 PPG 0.456522 0.763889
49 DCS 0.454545 0.670732
50 AQ3 0.447917 0.777778
51 PL8 0.44086 0.753247
52 9YM 0.43956 0.726027
53 RMT 0.421053 0.760563
54 1D0 0.418367 0.767123
55 7B9 0.416667 0.783784
56 AN7 0.409639 0.712121
57 FOO 0.404762 0.746269
58 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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