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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 NVA 0.538462 0.740741
10 API 0.538462 0.689655
11 DBB 0.5 0.692308
12 2RA 0.5 0.75
13 GLN 0.5 0.645161
14 ABA 0.5 0.692308
15 DSN 0.5 0.777778
16 DGN 0.5 0.645161
17 SER 0.5 0.777778
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 DAS 0.461538 0.655172
24 ASP 0.461538 0.655172
25 MSE 0.451613 0.65625
26 UN1 0.451613 0.689655
27 MET 0.451613 0.733333
28 11C 0.451613 0.689655
29 MED 0.451613 0.733333
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 AS2 0.428571 0.642857
35 LEU 0.428571 0.642857
36 KKA 0.428571 0.685714
37 ONH 0.424242 0.611111
38 NPI 0.424242 0.666667
39 6CL 0.411765 0.666667
40 2FM 0.411765 0.758621
41 26P 0.411765 0.625
42 VUR 0.410256 0.657143
43 3GC 0.410256 0.705882
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: 64
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 LPI 0.785714 0.924242
7 QLP 0.785714 0.909091
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 PDD 0.685714 0.888889
16 PDA 0.685714 0.888889
17 PP3 0.685714 0.888889
18 2BO 0.666667 0.888889
19 2BK 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 PSZ 0.511905 0.811594
38 3LM 0.511905 0.852941
39 PXP 0.507246 0.774194
40 PMH 0.5 0.688312
41 PMP 0.5 0.83871
42 PXG 0.494253 0.846154
43 RW2 0.494253 0.865672
44 PL2 0.488095 0.823529
45 DCS 0.488095 0.75
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 F0G 0.421687 0.75
54 CAN PLP 0.417582 0.865672
55 KOU 0.416667 0.8125
56 PL6 0.413793 0.796875
57 0JO 0.409639 0.731343
58 FEJ 0.409091 0.742424
59 Z98 0.409091 0.846154
60 PPG 0.408602 0.863636
61 PLP CYS 0.406977 0.904762
62 RMT 0.404255 0.779412
63 1D0 0.402062 0.838235
64 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 EPC 0.597015 0.907407
9 AN7 0.597015 0.854545
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 P3D 0.547945 0.723077
20 HCP 0.547945 0.786885
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 5DK 0.52439 0.769231
26 EQJ 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 PLP PHE 0.448276 0.779661
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 P1T 0.423077 0.784615
41 PP3 0.423077 0.777778
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 TLP 0.4125 0.777778
50 2BK 0.4125 0.777778
51 9TD 0.412371 0.714286
52 PLP 142 0.410526 0.731343
53 PPG 0.409091 0.784615
54 PPD 0.407407 0.738462
55 C6P 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: 157
This union binding pocket(no: 1) in the query (biounit: 5x30.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4RKC PMP 1.25628
2 5MB4 NDG 1.25628
3 5MB4 NAG 1.25628
4 1AJS PLA 1.50754
5 1FDJ 13P 1.65289
6 5CQG 55C 1.75879
7 6C3C EJ1 1.75879
8 6FYQ PLP 1.75879
9 4UOX PLP 1.75879
10 4WOE 3S5 1.75879
11 6CBO DOW 1.75879
12 4AOA IK2 2.01005
13 3BWN PMP 2.04604
14 3BWN PMP PHE 2.04604
15 2PO3 T4K 2.12264
16 4E3Q PMP 2.26131
17 4ZM4 PLP 2.26131
18 2HHP FLC 2.26131
19 4ZSY RW2 2.26131
20 1C7O PPG 2.26131
21 5KGS 6SR 2.51256
22 5DDW 5B6 2.51256
23 4UHO PLP 2.51256
24 4B98 PXG 2.51256
25 1TOI HCI 2.52525
26 1TDU DUR 2.64151
27 1M32 PLP 2.73224
28 6DND PLP 2.76382
29 5WYF ILP 2.76382
30 6CZY PMP 2.76382
31 2Z49 AMG 2.76382
32 1R6W 164 2.79503
33 2OFD NGA 2.8169
34 5U23 TQP 2.87958
35 5GVR LMR 2.99145
36 4KWI NAP 3.04183
37 4KWI 1TJ 3.04183
38 5GVL GI8 3.26633
39 5GVL PLG 3.26633
40 4ADC PLP 3.26633
41 4ZUL UN1 3.26633
42 5Y2W PGA 3.4188
43 1M7Y PPG 3.51759
44 5G09 6DF 3.51759
45 2X5F PLP 3.51759
46 4CS4 AXZ 3.64964
47 4JE5 PMP 3.76884
48 5WS9 OXL 3.76884
49 2CJH AKG 3.76884
50 4JE5 PLP 3.76884
51 4OKD GLC GLC GLC 3.76884
52 5MDH MAK 3.9039
53 2X5D PLP 4.0201
54 2R0H CTO 4.26829
55 2WZF BGC 4.27136
56 3VP6 HLD 4.52261
57 1MLY ACZ PLP 4.52261
58 2Q6B HR2 4.52261
59 5W19 9TD 4.77387
60 1O69 X04 4.82234
61 4WXG 2BO 5.02513
62 1ZC9 PMP 5.02513
63 6C92 EQJ 5.05319
64 6C8T EQJ 5.05319
65 6C9B EGV 5.05319
66 1M1B SPV 5.08475
67 2CFC KPC 5.2
68 4BA5 PXG 5.27638
69 4ARE FLC 5.27638
70 4AZJ SEP PLP 5.27778
71 2FNU PMP UD1 5.33333
72 1OFZ FUC 5.44872
73 6HL7 CP 5.45977
74 4FHT DHB 5.73248
75 2TPL HPP 5.77889
76 3EW2 BTN 5.92593
77 2R5E QLP 6.03015
78 2R5C C6P 6.03015
79 3EI9 PL6 6.03015
80 1OXO IK2 6.03015
81 3PDB PMP 6.03015
82 3PD6 PMP 6.03015
83 1GDE GLU PLP 6.16967
84 5IWQ PLP 6.28141
85 2ZYJ PGU 6.29723
86 6GPC ARG 6.34921
87 6ECG PM9 6.78392
88 1U26 IHS 6.82493
89 3QDV A2G 6.99301
90 3QDW A2G 6.99301
91 6CD1 PLG 7.03518
92 6CD1 PLS 7.03518
93 4FL0 PLP 7.28643
94 5K8B PDG 7.53769
95 1SFF IK2 7.78894
96 5YKT PMP 7.78894
97 1WYV PLP AOA 7.78894
98 5W70 9YM 8.0402
99 5WHU SIA GAL GLC 8.05369
100 3HQP OXL 8.29146
101 3FQ8 PMP 8.29146
102 1GEX PLP HSA 8.42697
103 3A8U PLP 8.54271
104 1DJ9 KAM 8.59375
105 4RW3 DKA 8.9404
106 4R5Z SIN 8.99183
107 4R5Z PMP 8.99183
108 1LC8 33P 9.06593
109 2O1C PPV 9.33333
110 1ELU PDA 9.48718
111 4M2K PLP 9.799
112 3BS8 PMP 9.799
113 5W71 9YM 10.3015
114 5W71 PLP 10.3015
115 1XI9 PLP 10.5528
116 6EWR PMP 10.804
117 3CQ5 PMP 10.8401
118 4ZAH T5K 10.8586
119 4AG9 16G 10.9091
120 1DFO PLG 11.3065
121 2HOX P1T 11.809
122 5OF1 SAL 11.9048
123 2ZC0 PMP 12.0603
124 1U08 PLP 12.1762
125 1Z17 ILE 12.5
126 1UU1 PMP HSA 12.5373
127 1VJO PLP 12.7226
128 2Z9V PXM 12.7551
129 5VEQ PMP 12.8141
130 3B8X G4M 12.8205
131 3ZRR PXG 13.0208
132 3FRK TQP 13.1367
133 3DR4 G4M 13.555
134 1GCK ASP PLP 14.2857
135 5TIV A3P 14.6245
136 4K2M O1G 15.0754
137 1B9I PXG 15.2062
138 5TXR PLP 15.5779
139 2WK9 PLG 15.6812
140 2WK9 PLP 15.6812
141 3NUB UD0 16.7131
142 2R2N KYN 17.0854
143 2R2N PMP 17.0854
144 1MDZ DCS 18.3206
145 1MDZ PLP 18.3206
146 2OGA PGU 20.603
147 1FC4 AKB PLP 23.3668
148 2XBN PMP 25.6281
149 4JN6 OXL 28.4314
150 1LW4 PLP 30.2594
151 1LW4 TLP 30.2594
152 2Q8E OGA 31.25
153 3WGC PLG 32.8446
154 4LNL 2BO 33.6336
155 4LNL 2BK 33.6336
156 4LNL PLG 33.6336
157 1CL2 PPG 46.5823
Pocket No.: 2; Query (leader) PDB : 5X30; Ligand: 4LM; Similar sites found with APoc: 152
This union binding pocket(no: 2) in the query (biounit: 5x30.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJD TFP None
2 4RKC PMP 1.25628
3 1AJS PLA 1.50754
4 6CBN OZY 1.50754
5 1FDJ 13P 1.65289
6 6C3C EJ1 1.75879
7 6FYQ PLP 1.75879
8 5CQG 55C 1.75879
9 6CBO DOW 1.75879
10 4UOX PLP 1.75879
11 6F5W KG1 1.89702
12 4AOA IK2 2.01005
13 3BWN PMP 2.04604
14 3BWN PMP PHE 2.04604
15 2PO3 T4K 2.12264
16 4ZM4 PLP 2.26131
17 4ZSY RW2 2.26131
18 2HHP FLC 2.26131
19 1C7O PPG 2.26131
20 4E3Q PMP 2.26131
21 5KGS 6SR 2.51256
22 5DDW 5B6 2.51256
23 4UHO PLP 2.51256
24 4B98 PXG 2.51256
25 1TOI HCI 2.52525
26 1A8U BEZ 2.52708
27 1M32 PLP 2.73224
28 5WYF ILP 2.76382
29 2J0W ASP 2.76382
30 2ITM XUL 2.76382
31 6DND PLP 2.76382
32 2OFD NGA 2.8169
33 5U23 TQP 2.87958
34 1V97 MTE 2.92793
35 5GVR LMR 2.99145
36 5X8G S0N 3.01508
37 4KWI NAP 3.04183
38 4KWI 1TJ 3.04183
39 3K6V CIT 3.10734
40 5GVL PLG 3.26633
41 5GVL GI8 3.26633
42 4ADC PLP 3.26633
43 4ZUL UN1 3.26633
44 5G09 6DF 3.51759
45 1M7Y PPG 3.51759
46 2X5F PLP 3.51759
47 4JE5 PMP 3.76884
48 4JE5 PLP 3.76884
49 4OKD GLC GLC GLC 3.76884
50 2OG2 MLI 3.89972
51 5MDH MAK 3.9039
52 2X5D PLP 4.0201
53 3VZS NAP 4.28016
54 3VZS CAA 4.28016
55 3K7S R52 4.46927
56 3VP6 HLD 4.52261
57 1MLY ACZ PLP 4.52261
58 5H06 MAL 4.52261
59 3QPB URA 4.60993
60 5W19 9TD 4.77387
61 1O69 X04 4.82234
62 4WXG 2BO 5.02513
63 1ZC9 PMP 5.02513
64 6C92 EQJ 5.05319
65 6C8T EQJ 5.05319
66 6C9B EGV 5.05319
67 1M1B SPV 5.08475
68 4BA5 PXG 5.27638
69 2FNU PMP UD1 5.33333
70 1OFZ FUC 5.44872
71 4FHT DHB 5.73248
72 2TPL HPP 5.77889
73 2R5E QLP 6.03015
74 2R5C C6P 6.03015
75 3EI9 PL6 6.03015
76 1OXO IK2 6.03015
77 3PDB PMP 6.03015
78 3PD6 PMP 6.03015
79 1GDE GLU PLP 6.16967
80 5IWQ PLP 6.28141
81 2ZYJ PGU 6.29723
82 6GPC ARG 6.34921
83 6FWH 5LD 6.59898
84 6ECG PM9 6.78392
85 1U26 IHS 6.82493
86 3QDV A2G 6.99301
87 3QDW A2G 6.99301
88 6CD1 PLG 7.03518
89 6CD1 PLS 7.03518
90 5GWT SIN 7.19424
91 4FL0 PLP 7.28643
92 5K8B PDG 7.53769
93 1SFF IK2 7.78894
94 5YKT PMP 7.78894
95 1WYV PLP AOA 7.78894
96 5W70 9YM 8.0402
97 5WHU SIA GAL GLC 8.05369
98 3HQP OXL 8.29146
99 3FQ8 PMP 8.29146
100 1GEX PLP HSA 8.42697
101 3A8U PLP 8.54271
102 1DJ9 KAM 8.59375
103 4RW3 DKA 8.9404
104 4R5Z SIN 8.99183
105 4R5Z PMP 8.99183
106 1LC8 33P 9.06593
107 4M2K PLP 9.799
108 3BS8 PMP 9.799
109 5W71 9YM 10.3015
110 5W71 PLP 10.3015
111 1XI9 PLP 10.5528
112 6EWR PMP 10.804
113 3CQ5 PMP 10.8401
114 4ZAH T5K 10.8586
115 1DFO PLG 11.3065
116 2HOX P1T 11.809
117 5OF1 SAL 11.9048
118 2ZC0 PMP 12.0603
119 1U08 PLP 12.1762
120 1TE2 PGA 12.3894
121 1Z17 ILE 12.5
122 1UU1 PMP HSA 12.5373
123 1VJO PLP 12.7226
124 2Z9V PXM 12.7551
125 5VEQ PMP 12.8141
126 3B8X G4M 12.8205
127 3ZRR PXG 13.0208
128 3FRK TQP 13.1367
129 3DR4 G4M 13.555
130 1GCK ASP PLP 14.2857
131 5TIV A3P 14.6245
132 4K2M O1G 15.0754
133 1B9I PXG 15.2062
134 5TXR PLP 15.5779
135 2WK9 PLG 15.6812
136 2WK9 PLP 15.6812
137 3NUB UD0 16.7131
138 2R2N KYN 17.0854
139 2R2N PMP 17.0854
140 1MDZ DCS 18.3206
141 1MDZ PLP 18.3206
142 2OGA PGU 20.603
143 1FC4 AKB PLP 23.3668
144 2XBN PMP 25.6281
145 4JN6 OXL 28.4314
146 1LW4 PLP 30.2594
147 1LW4 TLP 30.2594
148 3WGC PLG 32.8446
149 4LNL 2BO 33.6336
150 4LNL 2BK 33.6336
151 4LNL PLG 33.6336
152 1CL2 PPG 46.5823
Pocket No.: 3; Query (leader) PDB : 5X30; Ligand: HCS; Similar sites found with APoc: 40
This union binding pocket(no: 3) in the query (biounit: 5x30.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 3VCY UD1 1.25628
2 1MOQ GLP 1.3587
3 4ASE AV9 1.41643
4 2VZ0 D64 1.86567
5 2VZ0 NAP 1.86567
6 1V9N NDP 1.94444
7 1Z2I NAD 1.95531
8 2XG9 NOJ GLC 2.01005
9 1Q6D GLC GLC 2.26131
10 1X7D NAD 2.57143
11 5YJI SAH 2.8169
12 5YJI 8WO 2.8169
13 5YJF SAH 2.8169
14 5YJF 8WO 2.8169
15 5KD6 6C7 3.01508
16 1U1F 183 3.125
17 1SW0 PGA 3.22581
18 4ZDC CO8 3.33333
19 1F2U ATP 3.3557
20 2OZL TPP 3.56164
21 4WAS COO 3.57143
22 1QDS PGA 3.58566
23 2BTO GTP 3.7037
24 4YDQ ANP 4.27136
25 4YDQ HFG 4.27136
26 4BI7 PGA 4.28016
27 4GAA BES 4.52261
28 5KOR GDP 4.77387
29 2CFC NAD 5.2
30 4XGX ADP 5.88235
31 5ECP JAA 6.03015
32 5ECP ATP 6.03015
33 5ECP MET 6.03015
34 3OJF IMJ 6.22568
35 2X06 NAD 6.68605
36 4FJU NAI 7.40741
37 4YMZ 13P 10.757
38 5DTF 5CT 12.1739
39 1TRD PGH 14.4
40 1CL2 PPG 46.5823
Pocket No.: 4; Query (leader) PDB : 5X30; Ligand: HCS; Similar sites found with APoc: 19
This union binding pocket(no: 4) in the query (biounit: 5x30.bio1) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 5KK4 44E None
2 2ZAT NAP 2.30769
3 4ZGS NAD 2.59067
4 2ZIF SAM 2.6936
5 3EBL GA4 3.0137
6 4P6G 2FZ 3.09735
7 5JPH COA 4.16667
8 1PI5 SM2 4.46927
9 2BD0 NAP 4.5082
10 3QPB R1P 4.60993
11 3BJE R1P 4.87106
12 1NFQ NAI 5
13 5OQW A4E 5.51181
14 1KQB BEZ 6.91244
15 2E27 AB0 7.93651
16 4MTI 2DX 8.69565
17 6APV 3L4 8.7963
18 2W9S NDP 9.31677
19 2ZSH GA3 12.7273
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