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Receptor
PDB id Resolution Class Description Source Keywords
1MDZ 2.07 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF ARNB AMINOTRANSFERASE WITH CYCLOSERINE PYRIDOXAL 5' PHOSPHATE SALMONELLA TYPHIMURIUM TYPE 1 AMINOTRANSFERASE FOLD TRANSFERASE
Ref.: STRUCTURAL STUDIES OF SALMONELLA TYPHIMURIUM ARNB ( AMINOTRANSFERASE: A 4-AMINO-4-DEOXY-L-ARABINOSE LIPOPOLYSACCHARIDE MODIFYING ENZYME STRUCTURE V. 10 1569 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DCS A:400;
Valid;
none;
submit data
333.234 C11 H16 N3 O7 P Cc1c(...
PLP A:401;
Valid;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1MDZ 2.07 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF ARNB AMINOTRANSFERASE WITH CYCLOSERINE PYRIDOXAL 5' PHOSPHATE SALMONELLA TYPHIMURIUM TYPE 1 AMINOTRANSFERASE FOLD TRANSFERASE
Ref.: STRUCTURAL STUDIES OF SALMONELLA TYPHIMURIUM ARNB ( AMINOTRANSFERASE: A 4-AMINO-4-DEOXY-L-ARABINOSE LIPOPOLYSACCHARIDE MODIFYING ENZYME STRUCTURE V. 10 1569 2002
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 4OCA - 2QR C22 H33 N4 O20 P3 Cc1c(c(c(c....
2 1MDX - AKG C5 H6 O5 C(CC(=O)O)....
3 1MDO - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
4 1MDZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 4OCA - 2QR C22 H33 N4 O20 P3 Cc1c(c(c(c....
2 1MDX - AKG C5 H6 O5 C(CC(=O)O)....
3 1MDO - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
4 1MDZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 4OCA - 2QR C22 H33 N4 O20 P3 Cc1c(c(c(c....
2 1MDX - AKG C5 H6 O5 C(CC(=O)O)....
3 1MDO - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
4 1MDZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DCS; Similar ligands found: 54
No: Ligand ECFP6 Tc MDL keys Tc
1 DCS 1 1
2 7TS 0.5625 0.933333
3 IN5 0.546667 0.72973
4 9YM 0.535714 0.797297
5 PMH 0.531646 0.905405
6 5PA 0.531646 0.763158
7 PLG 0.526316 0.746667
8 PL8 0.517241 0.797468
9 PLS 0.5125 0.794521
10 2BK 0.5125 0.756757
11 2BO 0.5125 0.756757
12 TLP 0.5125 0.756757
13 PDA 0.506329 0.733333
14 PP3 0.506329 0.733333
15 P1T 0.506329 0.74026
16 PDD 0.506329 0.733333
17 C6P 0.506173 0.77027
18 PPD 0.506173 0.77027
19 LCS 0.5 0.932432
20 PLA 0.5 0.730769
21 33P 0.5 0.697368
22 PXP 0.5 0.680556
23 PY5 0.5 0.730769
24 IK2 0.5 0.810811
25 PY6 0.494118 0.7125
26 PMP 0.492958 0.712329
27 7B9 0.488889 0.759494
28 RW2 0.488636 0.74359
29 PSZ 0.488372 0.74359
30 N5F 0.488372 0.74026
31 PDG 0.488095 0.75
32 ILP 0.488095 0.714286
33 7XF 0.488095 0.75
34 PGU 0.488095 0.75
35 GT1 0.486111 0.618421
36 PMG 0.482353 0.7125
37 LPI 0.482353 0.703704
38 QLP 0.482353 0.779221
39 ORX 0.471264 0.74026
40 CBA 0.470588 0.821918
41 PE1 0.465909 0.74026
42 PL2 0.465116 0.666667
43 HEY 0.45977 0.708861
44 76U 0.45977 0.717949
45 PXG 0.455556 0.723684
46 PL4 0.455556 0.74026
47 EA5 0.454545 0.74359
48 3LM 0.454545 0.670732
49 DOW 0.433962 0.792208
50 KAM 0.430108 0.696203
51 AQ3 0.427083 0.776316
52 0LD 0.4 0.77907
53 RMT 0.4 0.692308
54 PZP 0.4 0.621622
Ligand no: 2; Ligand: PLP; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 F0G 0.564516 0.865385
12 MPM 0.564516 0.814815
13 FEV 0.555556 0.803571
14 KOU 0.555556 0.836364
15 HCP 0.546875 0.77193
16 EVM 0.546875 0.821429
17 6DF 0.545455 0.811321
18 PXL 0.541667 0.659574
19 Z98 0.537313 0.75
20 PXP 0.537037 0.862745
21 PMP 0.527273 0.767857
22 P0P 0.527273 0.916667
23 PL6 0.522388 0.818182
24 GT1 0.517857 0.830189
25 PFM 0.514706 0.803571
26 FEJ 0.514706 0.851852
27 LLP 0.5 0.737705
28 P70 0.5 0.833333
29 PUS 0.479452 0.707692
30 PL5 0.479452 0.775862
31 MPL 0.473684 0.836364
32 PLG 0.46875 0.75
33 IN5 0.46875 0.758621
34 P89 0.466667 0.714286
35 PLP PUT 0.463768 0.672131
36 EQJ 0.460526 0.725806
37 5DK 0.460526 0.725806
38 O1G 0.454545 0.75
39 PLT 0.439024 0.762712
40 X04 0.431034 0.851852
41 PDD 0.426471 0.762712
42 PP3 0.426471 0.762712
43 PDA 0.426471 0.762712
44 P1T 0.426471 0.714286
45 33P 0.42029 0.745763
46 IK2 0.42029 0.714286
47 TLP 0.414286 0.793103
48 2BK 0.414286 0.793103
49 PLS 0.414286 0.779661
50 2BO 0.414286 0.793103
51 5PA 0.414286 0.714286
52 PMH 0.414286 0.619718
53 9TD 0.413793 0.671642
54 PLP 999 0.410959 0.796296
55 PPD 0.408451 0.75
56 C6P 0.408451 0.75
57 QLP 0.405405 0.681818
58 MP5 0.403509 0.666667
59 PLA 0.402778 0.703125
60 PY5 0.402778 0.703125
61 HEY 0.4 0.703125
62 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1MDZ; Ligand: DCS; Similar sites found with APoc: 114
This union binding pocket(no: 1) in the query (biounit: 1mdz.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 5V8E CIT 1.61812
2 1PIG GLC GLC 1.78117
3 6FYQ PLP 1.78117
4 1GEX PLP HSA 1.96629
5 5IWQ PLP 2.03562
6 4UHO PLP 2.03562
7 4B98 PXG 2.03562
8 2Q8G AZX 2.03562
9 3L6C MLI 2.0649
10 1JS3 PLP 142 2.26337
11 6DND PLP 2.29008
12 4FL0 PLP 2.29008
13 1ZC9 PMP 2.29008
14 5YXC CIT 2.31481
15 1UU1 PMP HSA 2.38806
16 3MBI HSX 2.43902
17 1LC8 33P 2.47253
18 1MXG ACR 2.54453
19 2P3V SRT 2.73438
20 5YKT PMP 2.79898
21 1VJO PLP 3.05344
22 2FYF PLP 3.30789
23 4JE5 PLP 3.30789
24 4JE5 PMP 3.30789
25 6CD1 PLG 3.30789
26 6CD1 PLS 3.30789
27 4ZSY RW2 3.30789
28 3W9F I3P 3.46154
29 2Z9V PXM 3.57143
30 5NM7 GLY 3.7594
31 5ME4 HP4 4.0146
32 5YRG BGC GLC 4.22535
33 5YRF GLC GLC 4.22535
34 5YRL GLC GLC 4.22535
35 1DFO PLG 4.31655
36 5TXR PLP 4.3257
37 5G4J EXT 4.3257
38 1GPM CIT 4.3257
39 3TBK ANP 4.3257
40 4P83 U5P 4.3956
41 3AJ4 SEP 4.46429
42 4HVK PMP 4.71204
43 4WOH 4NP 4.81928
44 3PD6 PMP 4.83461
45 3PDB PMP 4.83461
46 4UOX PLP 4.83461
47 4UOX PUT 4.83461
48 4P86 5GP 4.91803
49 4DDY DN6 4.94297
50 5LV1 78T 5
51 3CQ5 PMP 5.14905
52 1PMO PLR 5.34351
53 1CL2 PPG 5.34351
54 3BS8 PMP 5.85242
55 1SFF IK2 5.85242
56 6C3C EJ1 6.10687
57 3A8U PLP 6.36132
58 1M32 PLP 6.55738
59 4ADC PLP 6.61578
60 1E5F PLP 6.87023
61 4BA5 PXG 7.12468
62 1WYV PLP AOA 7.37913
63 1LW4 PLP 8.06916
64 1LW4 TLP 8.06916
65 2XBN PMP 8.39695
66 1GCK ASP PLP 8.57143
67 2GUD MAN 9.01639
68 2HYR BGC GLC 9.01639
69 2GUC MAN 9.01639
70 2NUO BGC 9.01639
71 2HOX P1T 9.66921
72 5X2N ALA 9.77778
73 4LNL PLG 9.90991
74 4LNL 2BK 9.90991
75 4LNL 2BO 9.90991
76 1MLY ACZ PLP 10.4326
77 1DCP HBI 10.5769
78 4R5Z PMP 10.8992
79 6GNO XDI 11.1111
80 1IK4 PGH 11.1842
81 2ZC0 PMP 11.1959
82 4IYO 0JO 11.4504
83 4IY7 KOU 11.4504
84 4IY7 0JO 11.4504
85 2R5E QLP 11.4504
86 2R5C C6P 11.4504
87 4E1O PLP PVH 11.7048
88 2R2N PMP 11.9593
89 1ELU PDA 12.3077
90 3WGC PLG 12.3167
91 1FC4 AKB PLP 13.2316
92 4WXG 2BO 13.7405
93 5VEQ PMP 13.9949
94 3LN9 FLC 14.3885
95 1DJ9 KAM 15.1042
96 1GDE GLU PLP 16.9666
97 4RKC PMP 18.0662
98 5X30 4LM 18.3206
99 5X30 7XF 18.3206
100 5X2Z 3LM 18.3206
101 1U08 PLP 19.9482
102 5M3Z PLP 20.8651
103 5M3Z PY6 20.8651
104 5M3Z NLE 20.8651
105 5W70 9YM 38.1679
106 5W71 9YM 38.4224
107 5W71 PLP 38.4224
108 3B8X G4M 40
109 1B9I PXG 40.2036
110 5K8B PDG 41.4392
111 2PO3 T4K 47.3282
112 4ZAH T5K 47.8372
113 3FRK TQP 47.9893
114 4K2M O1G 48.0916
Pocket No.: 2; Query (leader) PDB : 1MDZ; Ligand: DCS; 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: 1mdz.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1MDZ; Ligand: PLP; Similar sites found with APoc: 114
This union binding pocket(no: 3) in the query (biounit: 1mdz.bio2) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 1PIG GLC GLC 1.78117
2 6FYQ PLP 1.78117
3 1GEX PLP HSA 1.96629
4 5IWQ PLP 2.03562
5 4UHO PLP 2.03562
6 4B98 PXG 2.03562
7 3L6C MLI 2.0649
8 1JS3 PLP 142 2.26337
9 6DND PLP 2.29008
10 4FL0 PLP 2.29008
11 1ZC9 PMP 2.29008
12 5YXC CIT 2.31481
13 1UU1 PMP HSA 2.38806
14 1LC8 33P 2.47253
15 1MXG ACR 2.54453
16 2P3V SRT 2.73438
17 5YKT PMP 2.79898
18 1VJO PLP 3.05344
19 2FYF PLP 3.30789
20 4JE5 PLP 3.30789
21 4JE5 PMP 3.30789
22 6CD1 PLS 3.30789
23 6CD1 PLG 3.30789
24 4ZSY RW2 3.30789
25 3W9F I3P 3.46154
26 3Q60 ATP 3.50404
27 2WQN ADP 3.54839
28 2Z9V PXM 3.57143
29 5NM7 GLY 3.7594
30 5ME4 HP4 4.0146
31 5YRG BGC GLC 4.22535
32 5YRF GLC GLC 4.22535
33 5YRL GLC GLC 4.22535
34 1DFO PLG 4.31655
35 5TXR PLP 4.3257
36 1GPM CIT 4.3257
37 3TBK ANP 4.3257
38 5G4J EXT 4.3257
39 4P83 U5P 4.3956
40 3AJ4 SEP 4.46429
41 1FHW I5P 4.65116
42 4HVK PMP 4.71204
43 4WOH 4NP 4.81928
44 3PD6 PMP 4.83461
45 3PDB PMP 4.83461
46 4UOX PLP 4.83461
47 4UOX PUT 4.83461
48 4P86 5GP 4.91803
49 4DDY DN6 4.94297
50 5LV1 78T 5
51 3CQ5 PMP 5.14905
52 1PMO PLR 5.34351
53 1CL2 PPG 5.34351
54 3BS8 PMP 5.85242
55 1SFF IK2 5.85242
56 6C3C EJ1 6.10687
57 3A8U PLP 6.36132
58 1M32 PLP 6.55738
59 4ADC PLP 6.61578
60 1E5F PLP 6.87023
61 4BA5 PXG 7.12468
62 1WYV PLP AOA 7.37913
63 1LW4 PLP 8.06916
64 1LW4 TLP 8.06916
65 2XBN PMP 8.39695
66 1GCK ASP PLP 8.57143
67 2GUD MAN 9.01639
68 2HYR BGC GLC 9.01639
69 2GUC MAN 9.01639
70 2NUO BGC 9.01639
71 2HOX P1T 9.66921
72 5X2N ALA 9.77778
73 4LNL PLG 9.90991
74 4LNL 2BO 9.90991
75 4LNL 2BK 9.90991
76 1MLY ACZ PLP 10.4326
77 1DCP HBI 10.5769
78 4R5Z PMP 10.8992
79 6GNO XDI 11.1111
80 2ZC0 PMP 11.1959
81 3AB4 THR 11.236
82 4IYO 0JO 11.4504
83 4IY7 0JO 11.4504
84 4IY7 KOU 11.4504
85 2R5E QLP 11.4504
86 2R5C C6P 11.4504
87 4E1O PLP PVH 11.7048
88 2R2N PMP 11.9593
89 1ELU PDA 12.3077
90 3WGC PLG 12.3167
91 1FC4 AKB PLP 13.2316
92 4WXG 2BO 13.7405
93 5VEQ PMP 13.9949
94 3LN9 FLC 14.3885
95 1DJ9 KAM 15.1042
96 1GDE GLU PLP 16.9666
97 4RKC PMP 18.0662
98 5X30 4LM 18.3206
99 5X30 7XF 18.3206
100 5X2Z 3LM 18.3206
101 1U08 PLP 19.9482
102 5M3Z PLP 20.8651
103 5M3Z PY6 20.8651
104 5M3Z NLE 20.8651
105 5W70 9YM 38.1679
106 5W71 9YM 38.4224
107 5W71 PLP 38.4224
108 3B8X G4M 40
109 1B9I PXG 40.2036
110 5K8B PDG 41.4392
111 2PO3 T4K 47.3282
112 4ZAH T5K 47.8372
113 3FRK TQP 47.9893
114 4K2M O1G 48.0916
Pocket No.: 4; Query (leader) PDB : 1MDZ; Ligand: PLP; 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: 1mdz.bio2) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1MDZ; Ligand: DCS; Similar sites found with APoc: 2
This union binding pocket(no: 5) in the query (biounit: 1mdz.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 2P1E LAC 3.85852
2 4L80 OXL 5.74713
Pocket No.: 6; Query (leader) PDB : 1MDZ; Ligand: PLP; Similar sites found with APoc: 1
This union binding pocket(no: 6) in the query (biounit: 1mdz.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 2P1E LAC 3.85852
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