Receptor
PDB id Resolution Class Description Source Keywords
5X30 1.7 Å EC: 4.4.1.11 CRYSTAL STRUCTURE OF PSEUDOMONAS PUTIDA METHIONINE GAMMA-LYA MUTANT WITH L-HOMOCYSTEINE 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
HCS A:501;
C:501;
Valid;
Valid;
none;
none;
submit data
135.185 C4 H9 N O2 S C(CS)...
7XF D:501;
Valid;
none;
submit data
366.327 C12 H19 N2 O7 P S Cc1c(...
4LM B:401;
Valid;
none;
submit data
330.23 C12 H15 N2 O7 P C/C=C...
H2S B:402;
Invalid;
none;
submit data
34.081 H2 S S
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5X30 1.7 Å EC: 4.4.1.11 CRYSTAL STRUCTURE OF PSEUDOMONAS PUTIDA METHIONINE GAMMA-LYA MUTANT WITH L-HOMOCYSTEINE 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 (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5X30 - 7XF C12 H19 N2 O7 P S 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 5X30 - 7XF C12 H19 N2 O7 P S 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 2 families.
1 5X30 - 7XF C12 H19 N2 O7 P S Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HCS; Similar ligands found: 46
No: Ligand ECFP6 Tc MDL keys Tc
1 HCS 1 1
2 DCY 0.608696 0.916667
3 CYS 0.608696 0.916667
4 DAB 0.56 0.851852
5 HSE 0.56 0.821429
6 GGL 0.555556 0.714286
7 DGL 0.555556 0.714286
8 GLU 0.555556 0.714286
9 API 0.538462 0.689655
10 NVA 0.538462 0.740741
11 2RA 0.5 0.75
12 ABA 0.5 0.692308
13 DBB 0.5 0.692308
14 DSN 0.5 0.777778
15 DGN 0.5 0.645161
16 SER 0.5 0.777778
17 GLN 0.5 0.645161
18 ORN 0.482759 0.814815
19 C2N 0.48 0.730769
20 NLE 0.466667 0.689655
21 ONL 0.466667 0.645161
22 CSS 0.464286 0.75
23 ASP 0.461538 0.655172
24 DAS 0.461538 0.655172
25 UN1 0.451613 0.689655
26 MED 0.451613 0.733333
27 MET 0.451613 0.733333
28 11C 0.451613 0.689655
29 MSE 0.451613 0.65625
30 DLY 0.451613 0.785714
31 LYS 0.4375 0.758621
32 DHH 0.4375 0.666667
33 CSO 0.428571 0.636364
34 KKA 0.428571 0.685714
35 LEU 0.428571 0.642857
36 AS2 0.428571 0.642857
37 NPI 0.424242 0.666667
38 ONH 0.424242 0.611111
39 26P 0.411765 0.625
40 6CL 0.411765 0.666667
41 2FM 0.411765 0.758621
42 3GC 0.410256 0.705882
43 VUR 0.410256 0.657143
44 HL5 0.40625 0.75
45 CIR 0.4 0.611111
46 MF3 0.4 0.733333
Ligand no: 2; Ligand: 7XF; Similar ligands found: 66
No: Ligand ECFP6 Tc MDL keys Tc
1 7XF 1 1
2 PY5 0.820895 0.9375
3 C6P 0.80597 0.967213
4 PDG 0.797101 0.967742
5 PGU 0.797101 0.967742
6 QLP 0.785714 0.909091
7 LPI 0.785714 0.924242
8 PY6 0.774648 0.909091
9 PLS 0.764706 0.935484
10 N5F 0.763889 0.952381
11 ORX 0.763889 0.952381
12 PPD 0.753623 0.935484
13 PE1 0.753425 0.952381
14 PL4 0.733333 0.952381
15 PDA 0.685714 0.888889
16 PP3 0.685714 0.888889
17 PDD 0.685714 0.888889
18 2BK 0.666667 0.888889
19 2BO 0.666667 0.888889
20 TLP 0.666667 0.888889
21 ILP 0.653333 0.890625
22 IN5 0.619718 0.857143
23 AQ3 0.619048 0.878788
24 76U 0.615385 0.921875
25 PLG 0.597222 0.904762
26 CBA 0.589744 0.848485
27 EA5 0.5875 0.923077
28 P1T 0.573333 0.892308
29 IK2 0.565789 0.863636
30 5PA 0.558442 0.921875
31 KAM 0.552941 0.892308
32 33P 0.545455 0.815385
33 PLA 0.544304 0.878788
34 PMG 0.52439 0.909091
35 HEY 0.518072 0.907692
36 GT1 0.514286 0.69697
37 3LM 0.511905 0.852941
38 PSZ 0.511905 0.811594
39 PXP 0.507246 0.774194
40 CKT 0.506329 0.888889
41 PMH 0.5 0.688312
42 PMP 0.5 0.83871
43 PXG 0.494253 0.846154
44 RW2 0.494253 0.865672
45 DCS 0.488095 0.75
46 PL2 0.488095 0.823529
47 DN9 0.477778 0.857143
48 7TS 0.47619 0.696203
49 PPE 0.458824 0.952381
50 9YM 0.454545 0.820895
51 PL8 0.43956 0.794521
52 7B9 0.430108 0.828571
53 PLR 0.428571 0.68254
54 PLP 2KZ 0.423529 0.815385
55 F0G 0.421687 0.75
56 CAN PLP 0.417582 0.865672
57 KOU 0.416667 0.8125
58 PL6 0.413793 0.796875
59 0JO 0.409639 0.731343
60 FEJ 0.409091 0.742424
61 Z98 0.409091 0.846154
62 PPG 0.408602 0.863636
63 PLP CYS 0.406977 0.904762
64 RMT 0.404255 0.779412
65 1D0 0.402062 0.838235
66 P0P 0.4 0.725806
Ligand no: 3; Ligand: 4LM; Similar ligands found: 58
No: Ligand ECFP6 Tc MDL keys Tc
1 4LM 1 1
2 FEV 0.806452 0.981818
3 0JO 0.71875 0.946429
4 EVM 0.637681 0.833333
5 F0G 0.632353 0.944444
6 KOU 0.623188 0.847458
7 Z98 0.60274 0.793651
8 AN7 0.597015 0.854545
9 EPC 0.597015 0.907407
10 PL6 0.589041 0.862069
11 EXT 0.588235 0.813559
12 FEJ 0.581081 0.894737
13 PLP 0.57377 0.818182
14 FOO 0.565217 0.892857
15 PZP 0.564516 0.821429
16 LLP 0.564103 0.78125
17 PL5 0.564103 0.819672
18 MPM 0.56338 0.859649
19 HCP 0.547945 0.786885
20 P3D 0.547945 0.723077
21 PUS 0.544304 0.724638
22 P70 0.544304 0.877193
23 P89 0.530864 0.757576
24 6DF 0.526316 0.857143
25 EQJ 0.52439 0.769231
26 5DK 0.52439 0.769231
27 PFM 0.5 0.847458
28 PLT 0.483146 0.806452
29 PLP 999 0.481013 0.810345
30 PLP PUT 0.474359 0.692308
31 O1G 0.465116 0.765625
32 PMP 0.462687 0.725806
33 MET PLP 0.457831 0.746032
34 PLR 0.453125 0.8
35 CKT 0.435897 0.806452
36 PLP PVH 0.428571 0.731343
37 PXP 0.426471 0.716667
38 PDA 0.423077 0.777778
39 PDD 0.423077 0.777778
40 PP3 0.423077 0.777778
41 P1T 0.423077 0.784615
42 PLG 0.421053 0.738462
43 P0P 0.42029 0.785714
44 PY5 0.419753 0.720588
45 IK2 0.417722 0.705882
46 GT1 0.414286 0.721311
47 2BO 0.4125 0.777778
48 PLS 0.4125 0.738462
49 2BK 0.4125 0.777778
50 TLP 0.4125 0.777778
51 9TD 0.412371 0.714286
52 PLP 142 0.410526 0.731343
53 PPG 0.409091 0.784615
54 C6P 0.407407 0.738462
55 PPD 0.407407 0.738462
56 PLP MYB 0.406593 0.638889
57 PY6 0.4 0.7
58 HEY 0.4 0.772727
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5X30; Ligand: 7XF; 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: 5x30.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5X30; Ligand: 4LM; 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: 5x30.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5X30; Ligand: HCS; 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: 5x30.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5X30; Ligand: HCS; 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: 5x30.bio1) has 7 residues
No: Leader PDB Ligand Sequence Similarity
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