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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: 147
This union binding pocket(no: 1) in the query (biounit: 5x2z.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJD TFP None
2 4RKC PMP 1.25628
3 2WCI GSH 1.48148
4 1AJS PLA 1.50754
5 5CQG 55C 1.75879
6 6FYQ PLP 1.75879
7 4UOX PLP 1.75879
8 6C3C EJ1 1.75879
9 4WOE 3S5 1.75879
10 6CBO DOW 1.75879
11 6F5W KG1 1.89702
12 4AOA IK2 2.01005
13 3BWN PMP PHE 2.04604
14 3BWN PMP 2.04604
15 4E3Q PMP 2.26131
16 1C7O PPG 2.26131
17 4ZM4 PLP 2.26131
18 4ZSY RW2 2.26131
19 2HHP FLC 2.26131
20 3X01 AMP 2.29008
21 5DDW 5B6 2.51256
22 4UHO PLP 2.51256
23 5KGS 6SR 2.51256
24 4B98 PXG 2.51256
25 1TOI HCI 2.52525
26 1M32 PLP 2.73224
27 5WYF ILP 2.76382
28 2J0W ASP 2.76382
29 2Z49 AMG 2.76382
30 6DND PLP 2.76382
31 2OFD NGA 2.8169
32 5U23 TQP 2.87958
33 3OPT AKG 2.94906
34 5GVR LMR 2.99145
35 5GVL GI8 3.26633
36 5GVL PLG 3.26633
37 4ADC PLP 3.26633
38 2X5F PLP 3.51759
39 1M7Y PPG 3.51759
40 5G09 6DF 3.51759
41 4JE5 PLP 3.76884
42 4JE5 PMP 3.76884
43 5DO8 BGC 3.76884
44 2CJH AKG 3.76884
45 4OKD GLC GLC GLC 3.76884
46 5T4J PLP ABU 3.83562
47 2X5D PLP 4.0201
48 1T36 ORN 4.0201
49 3VMW ADA ADA ADA 4.29448
50 1MLY ACZ PLP 4.52261
51 3VP6 HLD 4.52261
52 5W3Y ACO 4.54545
53 4L9Z OXL 4.71976
54 5LNW HG3 4.74684
55 5LNW RP5 4.74684
56 5W19 9TD 4.77387
57 5AEW BNL 4.78723
58 4WXG 2BO 5.02513
59 1ZC9 PMP 5.02513
60 6C92 EQJ 5.05319
61 6C8T EQJ 5.05319
62 6C9B EGV 5.05319
63 2CFC KPC 5.2
64 4BA5 PXG 5.27638
65 2FNU PMP UD1 5.33333
66 3C8F MT2 5.71429
67 4FHT DHB 5.73248
68 2TPL HPP 5.77889
69 5A0U CHT 5.77889
70 3PD6 PMP 6.03015
71 3PDB PMP 6.03015
72 2R5E QLP 6.03015
73 2R5C C6P 6.03015
74 1OXO IK2 6.03015
75 3EI9 PL6 6.03015
76 1GDE GLU PLP 6.16967
77 5IWQ PLP 6.28141
78 2ZYJ PGU 6.29723
79 2OAT PFM 6.53266
80 6FWH 5LD 6.59898
81 6ECG PM9 6.78392
82 1U26 IHS 6.82493
83 3QDV A2G 6.99301
84 3QDW A2G 6.99301
85 6CD1 PLG 7.03518
86 6CD1 PLS 7.03518
87 4FL0 PLP 7.28643
88 5K8B PDG 7.53769
89 5YKT PMP 7.78894
90 1WYV PLP AOA 7.78894
91 1SFF IK2 7.78894
92 5W70 9YM 8.0402
93 1GEX PLP HSA 8.42697
94 3A8U PLP 8.54271
95 1DJ9 KAM 8.59375
96 4R5Z SIN 8.99183
97 4R5Z PMP 8.99183
98 1LC8 33P 9.06593
99 1ELU PDA 9.48718
100 4M2K PLP 9.799
101 3BS8 PMP 9.799
102 5W71 9YM 10.3015
103 5W71 PLP 10.3015
104 1XI9 PLP 10.5528
105 6EWR PMP 10.804
106 3CQ5 PMP 10.8401
107 4ZAH T5K 10.8586
108 4AG9 16G 10.9091
109 1DFO PLG 11.3065
110 1JQY A32 11.6505
111 2HOX P1T 11.809
112 5OF1 SAL 11.9048
113 2ZC0 PMP 12.0603
114 1U08 PLP 12.1762
115 1TE2 PGA 12.3894
116 1Z17 ILE 12.5
117 1UU1 PMP HSA 12.5373
118 1VJO PLP 12.5628
119 2Z9V PXM 12.7551
120 5VEQ PMP 12.8141
121 3B8X G4M 12.8205
122 4H69 10Y 12.8866
123 3ZRR PXG 13.0208
124 3FRK TQP 13.1367
125 3DR4 G4M 13.555
126 1GCK ASP PLP 14.2857
127 4K2M O1G 15.0754
128 1B9I PXG 15.2062
129 5TXR PLP 15.5779
130 2WK9 PLG 15.6812
131 2WK9 PLP 15.6812
132 3NUB UD0 16.7131
133 2R2N PMP 17.0854
134 2R2N KYN 17.0854
135 1MDZ DCS 18.3206
136 2OGA PGU 20.603
137 2IDO TMP 22.8916
138 1FC4 AKB PLP 23.3668
139 2XBN PMP 25.6281
140 1LW4 PLP 30.2594
141 1LW4 TLP 30.2594
142 2Q8E OGA 31.25
143 3WGC PLG 32.8446
144 4LNL PLG 33.6336
145 4LNL 2BK 33.6336
146 4LNL 2BO 33.6336
147 2YBP 2HG 41.6667
Pocket No.: 2; Query (leader) PDB : 5X2Z; Ligand: 3LM; Similar sites found with APoc: 41
This union binding pocket(no: 2) in the query (biounit: 5x2z.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4OKS 2T9 1.25628
2 6MVU K4V 1.50754
3 5A7V MAN 1.80412
4 5A7V BMA 1.80412
5 3B4Y FLC 1.96629
6 2PO3 T4K 2.12264
7 4D4U FUC NDG GAL FUC 2.53968
8 2A9W UMP 2.65152
9 3X27 TRP 2.98507
10 3HPY MCT 3.23625
11 5OFW 9TW 3.58744
12 1RZM PEP 3.84615
13 2OG2 MLI 3.89972
14 5N53 8NB 4.10256
15 1K4M CIT 4.22535
16 6GN6 GLC 4.27136
17 5EPA AKG 4.30108
18 3K7S R52 4.46927
19 3QPB URA 4.60993
20 3CEV ARG 4.68227
21 1M1B SPV 5.08475
22 5FQ0 FLC 5.26316
23 4ARE FLC 5.27638
24 1GXS DKA 5.6962
25 2Z77 HE7 5.7554
26 2HJ9 AI2 6.33484
27 2JBM SRT 6.35452
28 9ABP GLA 7.18954
29 9ABP GAL 7.18954
30 1YXM ADE 7.26073
31 4KQP GLN 7.75862
32 5WHU SIA GAL GLC 8.05369
33 3FQ8 PMP 8.29146
34 1PMO PLR 8.29146
35 2O1C PPV 9.33333
36 1ELU CSS 9.48718
37 2PNZ UDP 10.4693
38 4YKI GLY 11.3281
39 2HUI GLV 11.7048
40 5JWP AKG 31.5789
41 2OS2 OGA 45.4545
Pocket No.: 3; Query (leader) PDB : 5X2Z; Ligand: 3LM; Similar sites found with APoc: 9
This union binding pocket(no: 3) in the query (biounit: 5x2z.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1SZO CAX 2.33463
2 2Z48 A2G 2.76382
3 5FAW CHT 4.52261
4 4JLS 3ZE 4.60526
5 2CHT TSA 7.87402
6 2YJP CYS 9.96564
7 5W3X ACO 17.5
8 1MDZ PLP 18.3206
9 2XUM OGA 35
Pocket No.: 4; Query (leader) PDB : 5X2Z; Ligand: 3LM; Similar sites found with APoc: 21
This union binding pocket(no: 4) in the query (biounit: 5x2z.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 3TKY N7I 1.63043
2 4QM9 CYS 1.7341
3 5A2Z GTP 1.75879
4 5OSW DIU 1.75879
5 5AVF TAU 1.94553
6 3P3N AKG 2.00573
7 2C5S AMP 2.01005
8 3L6C MLI 2.0649
9 3ACH BGC BGC BGC BGC 2.46305
10 1TDU DUR 2.64151
11 3TFC PEP 3.63636
12 1GUI BGC BGC BGC BGC BGC BGC 4.51613
13 3CH6 NAP 4.8951
14 3CH6 311 4.8951
15 6BYF CIT 5.29412
16 4DDS 0J7 5.32319
17 3MMR ABH 6.78392
18 3AJ4 SEP 7.14286
19 3EHH ADP 7.79817
20 1H2M OGA 11.5385
21 1H2K OGA 14.6341
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