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: 45
No: Ligand ECFP6 Tc MDL keys Tc
1 HCS 1 1
2 CYS 0.608696 0.916667
3 DCY 0.608696 0.916667
4 DAB 0.56 0.851852
5 HSE 0.56 0.821429
6 GGL 0.555556 0.714286
7 GLU 0.555556 0.714286
8 DGL 0.555556 0.714286
9 NVA 0.538462 0.740741
10 API 0.538462 0.689655
11 DBB 0.5 0.692308
12 DSN 0.5 0.777778
13 DGN 0.5 0.645161
14 2RA 0.5 0.75
15 SER 0.5 0.777778
16 ABA 0.5 0.692308
17 GLN 0.5 0.645161
18 ORN 0.482759 0.814815
19 C2N 0.48 0.730769
20 ONL 0.466667 0.645161
21 NLE 0.466667 0.689655
22 CSS 0.464286 0.75
23 ASP 0.461538 0.655172
24 DAS 0.461538 0.655172
25 MET 0.451613 0.733333
26 MED 0.451613 0.733333
27 MSE 0.451613 0.65625
28 DLY 0.451613 0.785714
29 UN1 0.451613 0.689655
30 11C 0.451613 0.689655
31 DHH 0.4375 0.666667
32 LYS 0.4375 0.758621
33 KKA 0.428571 0.685714
34 LEU 0.428571 0.642857
35 CSO 0.428571 0.636364
36 AS2 0.428571 0.642857
37 NPI 0.424242 0.666667
38 ONH 0.424242 0.611111
39 6CL 0.411765 0.666667
40 26P 0.411765 0.625
41 2FM 0.411765 0.758621
42 3GC 0.410256 0.705882
43 VUR 0.410256 0.657143
44 CIR 0.4 0.611111
45 MF3 0.4 0.733333
Ligand no: 2; Ligand: 7XF; Similar ligands found: 60
No: Ligand ECFP6 Tc MDL keys Tc
1 7XF 1 1
2 PY5 0.820895 0.9375
3 C6P 0.80597 0.967213
4 PGU 0.797101 0.967742
5 PDG 0.797101 0.967742
6 QLP 0.785714 0.909091
7 PY6 0.774648 0.909091
8 PLS 0.764706 0.935484
9 ORX 0.763889 0.952381
10 N5F 0.763889 0.952381
11 PPD 0.753623 0.935484
12 PE1 0.753425 0.952381
13 PL4 0.733333 0.952381
14 PDA 0.685714 0.888889
15 PP3 0.685714 0.888889
16 PDD 0.685714 0.888889
17 2BK 0.666667 0.888889
18 2BO 0.666667 0.888889
19 TLP 0.666667 0.888889
20 ILP 0.653333 0.890625
21 IN5 0.619718 0.857143
22 AQ3 0.619048 0.878788
23 76U 0.615385 0.921875
24 PLG 0.597222 0.904762
25 CBA 0.589744 0.848485
26 EA5 0.5875 0.923077
27 P1T 0.573333 0.892308
28 IK2 0.565789 0.863636
29 5PA 0.558442 0.921875
30 KAM 0.552941 0.892308
31 33P 0.545455 0.815385
32 PLA 0.544304 0.878788
33 PMG 0.52439 0.909091
34 HEY 0.518072 0.907692
35 GT1 0.514286 0.69697
36 PSZ 0.511905 0.811594
37 3LM 0.511905 0.852941
38 PXP 0.507246 0.774194
39 PLP ALO 0.5 0.84375
40 PMP 0.5 0.83871
41 PMH 0.5 0.688312
42 PXG 0.494253 0.846154
43 RW2 0.494253 0.865672
44 DCS 0.488095 0.75
45 PL2 0.488095 0.823529
46 7TS 0.47619 0.696203
47 PPE 0.458824 0.952381
48 9YM 0.454545 0.820895
49 PL8 0.43956 0.794521
50 7B9 0.430108 0.828571
51 PLR 0.428571 0.68254
52 PLP 2KZ 0.423529 0.815385
53 CAN PLP 0.422222 0.878788
54 KOU 0.416667 0.8125
55 PL6 0.413793 0.796875
56 0JO 0.409639 0.731343
57 Z98 0.409091 0.846154
58 PPG 0.408602 0.863636
59 1D0 0.402062 0.838235
60 P0P 0.4 0.725806
Ligand no: 3; Ligand: 4LM; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 4LM 1 1
2 0JO 0.71875 0.946429
3 KOU 0.623188 0.847458
4 Z98 0.60274 0.793651
5 EPC 0.597015 0.907407
6 AN7 0.597015 0.854545
7 PL6 0.589041 0.862069
8 EXT 0.588235 0.813559
9 PLP 0.57377 0.818182
10 FOO 0.565217 0.892857
11 PZP 0.564516 0.821429
12 PL5 0.564103 0.819672
13 LLP 0.564103 0.78125
14 MPM 0.56338 0.859649
15 P3D 0.547945 0.723077
16 HCP 0.547945 0.786885
17 PUS 0.544304 0.724638
18 P89 0.530864 0.757576
19 6DF 0.526316 0.857143
20 5DK 0.52439 0.769231
21 PFM 0.5 0.847458
22 PLP ABU 0.5 0.754098
23 PLP PUT 0.493506 0.704918
24 PLT 0.483146 0.806452
25 O1G 0.465116 0.765625
26 PMP 0.462687 0.725806
27 PLR 0.453125 0.8
28 PLP PHE 0.448276 0.779661
29 PLP PVH 0.428571 0.731343
30 PXP 0.426471 0.716667
31 PDA 0.423077 0.777778
32 PDD 0.423077 0.777778
33 P1T 0.423077 0.784615
34 PP3 0.423077 0.777778
35 PLG 0.421053 0.738462
36 P0P 0.42029 0.785714
37 PY5 0.419753 0.720588
38 IK2 0.417722 0.705882
39 GT1 0.414286 0.721311
40 PLS 0.4125 0.738462
41 2BO 0.4125 0.777778
42 TLP 0.4125 0.777778
43 2BK 0.4125 0.777778
44 PLP 142 0.410526 0.731343
45 PPG 0.409091 0.784615
46 PPD 0.407407 0.738462
47 C6P 0.407407 0.738462
48 PLP MYB 0.406593 0.638889
49 PY6 0.4 0.7
50 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: 88
This union binding pocket(no: 1) in the query (biounit: 5x30.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RKC PMP 0.0004325 0.44011 1.25628
2 1AJS PLA 0.0001687 0.47826 1.50754
3 4UOX PLP 0.001543 0.4064 1.75879
4 4AOA IK2 0.002498 0.40887 2.01005
5 3BWN PMP 0.00002142 0.53333 2.04604
6 3BWN PMP PHE 0.0002182 0.45136 2.04604
7 2PO3 T4K 0.005804 0.42438 2.12264
8 4ZM4 PLP 0.001802 0.43815 2.26131
9 4ZSY RW2 0.001698 0.41483 2.26131
10 1C7O PPG 0.004165 0.41178 2.26131
11 5KGS 6SR 0.001783 0.45788 2.51256
12 4UHO PLP 0.01021 0.42043 2.51256
13 4B98 PXG 0.002694 0.41403 2.51256
14 5DDW 5B6 0.0026 0.40558 2.51256
15 2G50 PYR 0.0237 0.40011 2.51256
16 1M32 PLP 0.02181 0.4049 2.73224
17 5WYF ILP 0.00125 0.43437 2.76382
18 2Z49 AMG 0.02828 0.40003 2.76382
19 5U23 TQP 0.0009055 0.45737 2.87958
20 3B1E P1T 0.001113 0.44775 3.06122
21 5GVL PLG 0.0007174 0.47218 3.26633
22 5GVL GI8 0.0007174 0.47218 3.26633
23 4ADC PLP 0.002661 0.43487 3.26633
24 5G09 6DF 0.0002689 0.46321 3.51759
25 2X5F PLP 0.0003032 0.43243 3.51759
26 4JE5 PLP 0.002493 0.40345 3.76884
27 4JE5 PMP 0.002507 0.40257 3.76884
28 5MDH MAK 0.01168 0.4184 3.9039
29 3VP6 HLD 0.0009036 0.44802 4.52261
30 1MLY ACZ PLP 0.003042 0.41572 4.52261
31 1ZC9 PMP 0.0006563 0.44433 5.02513
32 4WXG 2BO 0.00017 0.44105 5.02513
33 5DJ3 5DK 0.0005244 0.44851 5.05319
34 4BA5 PXG 0.000865 0.42842 5.27638
35 4AZJ SEP PLP 0.007202 0.40326 5.27778
36 2R5C C6P 0.00004009 0.4989 6.03015
37 2R5E QLP 0.00003228 0.49225 6.03015
38 3PD6 PMP 0.0002302 0.49087 6.03015
39 1OXO IK2 0.001214 0.46576 6.03015
40 3PDB PMP 0.0002577 0.44588 6.03015
41 3EI9 PL6 0.0002637 0.43458 6.03015
42 1GDE GLU PLP 0.0002023 0.46626 6.16967
43 5IWQ PLP 0.0004837 0.4697 6.28141
44 2ZYJ PGU 0.0006535 0.45765 6.29723
45 4FL0 PLP 0.0002488 0.44225 7.28643
46 5K8B PDG 0.0001314 0.48099 7.53769
47 1SFF IK2 0.002065 0.41624 7.78894
48 1WYV PLP AOA 0.003695 0.4076 7.78894
49 5W70 9YM 0.00009324 0.48307 8.0402
50 3FQ8 PMP 0.005684 0.41113 8.29146
51 1GEX PLP HSA 0.03361 0.40479 8.42697
52 1DJ9 KAM 0.00004386 0.48249 8.59375
53 4RW3 DKA 0.01158 0.42913 8.9404
54 4R5Z PMP 0.00009895 0.46012 8.99183
55 4R5Z SIN 0.00008076 0.43662 8.99183
56 1LC8 33P 0.01986 0.41735 9.06593
57 1ELU PDA 0.006271 0.40221 9.48718
58 5W71 9YM 0.00102 0.46616 10.3015
59 5W71 PLP 0.0002782 0.45536 10.3015
60 1XI9 PLP 0.0003491 0.42657 10.5528
61 3CQ5 PMP 0.00004613 0.53958 10.8401
62 4ZAH T5K 0.0004288 0.40823 10.8586
63 4AG9 16G 0.01239 0.40736 10.9091
64 1DFO PLG 0.0002256 0.4665 11.3065
65 2HOX P1T 0.00007718 0.48423 11.809
66 2ZC0 PMP 0.00008677 0.47783 12.0603
67 1U08 PLP 0.00001218 0.48547 12.1762
68 1Z17 ILE 0.01742 0.41064 12.5
69 1UU1 PMP HSA 0.0000767 0.48902 12.5373
70 3E2Y PMP 0.00001065 0.49484 12.8141
71 3DR4 G4M 0.0002166 0.4952 13.555
72 1GCK ASP PLP 0.00009413 0.48289 14.2857
73 4K2M O1G 0.0008133 0.42309 15.0754
74 1B9I PXG 0.02833 0.40562 15.2062
75 2WK9 PLG 0.00000132 0.58787 15.6812
76 2WK9 PLP 0.000004626 0.55943 15.6812
77 3NUB UD0 0.002423 0.43797 16.7131
78 2R2N PMP 0.0003087 0.47886 17.0854
79 1MDZ PLP 0.003035 0.43483 18.3206
80 1MDZ DCS 0.003234 0.43483 18.3206
81 2OGA PGU 0.00193 0.42816 20.603
82 1FC4 AKB PLP 0.0003493 0.45608 23.3668
83 2XBN PMP 0.00821 0.43466 25.6281
84 4JN6 OXL 0.009932 0.4177 28.4314
85 1LW4 PLP 0.000571 0.43682 30.2594
86 1LW4 TLP 0.001076 0.43511 30.2594
87 3WGC PLG 0.0002563 0.45106 32.8446
88 1CL2 PPG 0.00005576 0.52888 46.5823
Pocket No.: 2; Query (leader) PDB : 5X30; Ligand: 4LM; Similar sites found: 85
This union binding pocket(no: 2) in the query (biounit: 5x30.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RKC PMP 0.003931 0.40699 1.25628
2 1AJS PLA 0.0007282 0.45474 1.50754
3 4UOX PLP 0.001949 0.40904 1.75879
4 4AOA IK2 0.002515 0.41547 2.01005
5 3BWN PMP 0.0001353 0.49326 2.04604
6 3BWN PMP PHE 0.001321 0.41655 2.04604
7 2PO3 T4K 0.005095 0.43056 2.12264
8 4ZM4 PLP 0.003321 0.42389 2.26131
9 1C7O PPG 0.006088 0.40994 2.26131
10 4E3Q PMP 0.001748 0.40543 2.26131
11 5KGS 6SR 0.002683 0.45334 2.51256
12 4UHO PLP 0.01202 0.41493 2.51256
13 4B98 PXG 0.004483 0.4101 2.51256
14 5DDW 5B6 0.001927 0.40566 2.51256
15 2G50 PYR 0.02201 0.40167 2.51256
16 5WYF ILP 0.00145 0.43569 2.76382
17 5U23 TQP 0.0008098 0.4639 2.87958
18 5X8G S0N 0.03754 0.4002 3.01508
19 3B1E P1T 0.004586 0.41749 3.06122
20 5GVL GI8 0.0007919 0.47452 3.26633
21 5GVL PLG 0.0007919 0.47452 3.26633
22 4ADC PLP 0.003007 0.43031 3.26633
23 5G09 6DF 0.0001156 0.48416 3.51759
24 2X5F PLP 0.002145 0.40955 3.51759
25 5MDH MAK 0.01273 0.41461 3.9039
26 3K7S R52 0.01538 0.40094 4.46927
27 3VP6 HLD 0.001652 0.44049 4.52261
28 1MLY ACZ PLP 0.002593 0.42256 4.52261
29 1ZC9 PMP 0.0008284 0.44431 5.02513
30 4WXG 2BO 0.0002916 0.42749 5.02513
31 5DJ3 5DK 0.001504 0.43295 5.05319
32 4BA5 PXG 0.0005576 0.44378 5.27638
33 4FHT DHB 0.0232 0.40189 5.73248
34 2R5C C6P 0.0002356 0.47052 6.03015
35 2R5E QLP 0.0001785 0.45665 6.03015
36 3PD6 PMP 0.001953 0.44401 6.03015
37 1OXO IK2 0.004516 0.44244 6.03015
38 3PDB PMP 0.001276 0.42216 6.03015
39 3EI9 PL6 0.0008323 0.41282 6.03015
40 1GDE GLU PLP 0.001017 0.43191 6.16967
41 5IWQ PLP 0.003904 0.425 6.28141
42 2ZYJ PGU 0.002266 0.43748 6.29723
43 4FL0 PLP 0.001636 0.41442 7.28643
44 5K8B PDG 0.0001094 0.48962 7.53769
45 1SFF IK2 0.002173 0.41024 7.78894
46 1WYV PLP AOA 0.004895 0.40843 7.78894
47 5W70 9YM 0.00009291 0.48836 8.0402
48 3FQ8 PMP 0.008001 0.40798 8.29146
49 1GEX PLP HSA 0.04748 0.40004 8.42697
50 1DJ9 KAM 0.0001001 0.47593 8.59375
51 4RW3 DKA 0.01259 0.41943 8.9404
52 4R5Z PMP 0.0003037 0.43739 8.99183
53 4R5Z SIN 0.0002066 0.41878 8.99183
54 1LC8 33P 0.04577 0.40213 9.06593
55 5W71 9YM 0.0009994 0.47082 10.3015
56 5W71 PLP 0.0003756 0.45707 10.3015
57 1XI9 PLP 0.001542 0.40384 10.5528
58 3CQ5 PMP 0.0005908 0.4811 10.8401
59 4ZAH T5K 0.0003375 0.40585 10.8586
60 1DFO PLG 0.0003036 0.46566 11.3065
61 2HOX P1T 0.0003129 0.46286 11.809
62 2ZC0 PMP 0.0005589 0.44954 12.0603
63 1U08 PLP 0.0001163 0.45686 12.1762
64 1TE2 PGA 0.0256 0.40176 12.3894
65 1Z17 ILE 0.01812 0.40799 12.5
66 1UU1 PMP HSA 0.0003759 0.46368 12.5373
67 3E2Y PMP 0.00009521 0.46551 12.8141
68 3DR4 G4M 0.0001414 0.50885 13.555
69 1GCK ASP PLP 0.0003162 0.46488 14.2857
70 4K2M O1G 0.0007829 0.41837 15.0754
71 1B9I PXG 0.02779 0.40891 15.2062
72 2WK9 PLG 0.000001403 0.59361 15.6812
73 2WK9 PLP 0.000005623 0.56197 15.6812
74 3NUB UD0 0.001734 0.44859 16.7131
75 2R2N PMP 0.001151 0.44982 17.0854
76 1MDZ DCS 0.002601 0.44301 18.3206
77 1MDZ PLP 0.002693 0.44104 18.3206
78 2OGA PGU 0.001782 0.43367 20.603
79 1FC4 AKB PLP 0.001005 0.43234 23.3668
80 2XBN PMP 0.01478 0.42538 25.6281
81 4JN6 OXL 0.0118 0.41498 28.4314
82 1LW4 PLP 0.002439 0.41707 30.2594
83 1LW4 TLP 0.003495 0.41686 30.2594
84 3WGC PLG 0.0002756 0.45752 32.8446
85 1CL2 PPG 0.0001772 0.51015 46.5823
Pocket No.: 3; Query (leader) PDB : 5X30; Ligand: HCS; Similar sites found: 12
This union binding pocket(no: 3) in the query (biounit: 5x30.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VCY UD1 0.01866 0.41934 1.25628
2 1Z2I NAD 0.008598 0.435 1.95531
3 2XG9 NOJ GLC 0.01559 0.42885 2.01005
4 1Q6D GLC GLC 0.02354 0.41228 2.26131
5 1SW0 PGA 0.0148 0.40232 3.22581
6 2F7C CCU 0.0238 0.41402 3.43348
7 2OZL TPP 0.02471 0.40667 3.56164
8 5KOR GDP 0.007542 0.42846 4.77387
9 5ECP ATP 0.03312 0.41129 6.03015
10 5ECP JAA 0.03205 0.41129 6.03015
11 5ECP MET 0.03205 0.41129 6.03015
12 1TRD PGH 0.01492 0.40272 14.4
Pocket No.: 4; Query (leader) PDB : 5X30; Ligand: HCS; 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: 5x30.bio1) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback