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Receptor
PDB id Resolution Class Description Source Keywords
2JFZ 1.86 Å EC: 5.1.1.3 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE AND AN INHIBITOR HELICOBACTER PYLORI CELL WALL ISOMERASE CELL SHAPE GLUTAMATE RACEMASE PEPTIDOGLYCAN SYNTHESIS PEPTIDOGLYCAN BIOSYNTHESIS
Ref.: EXPLOITATION OF STRUCTURAL AND REGULATORY DIVERSITY IN GLUTAMATE RACEMASES NATURE V. 447 817 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
003 A:1256;
B:1256;
Valid;
Valid;
none;
none;
Ki = 5.8 uM
439.509 C26 H25 N5 O2 CC(C)...
DGL A:1257;
B:1257;
Valid;
Valid;
none;
none;
submit data
147.129 C5 H9 N O4 C(CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2JFZ 1.86 Å EC: 5.1.1.3 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE AND AN INHIBITOR HELICOBACTER PYLORI CELL WALL ISOMERASE CELL SHAPE GLUTAMATE RACEMASE PEPTIDOGLYCAN SYNTHESIS PEPTIDOGLYCAN BIOSYNTHESIS
Ref.: EXPLOITATION OF STRUCTURAL AND REGULATORY DIVERSITY IN GLUTAMATE RACEMASES NATURE V. 447 817 2007
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4B1F - KRH C25 H26 N6 O2 CC(C)CN1c2....
2 2JFY - DGL C5 H9 N O4 C(CC(=O)O)....
3 2JFZ Ki = 5.8 uM 003 C26 H25 N5 O2 CC(C)CN1c2....
4 2W4I ic50 = 0.5 uM VGA C22 H19 N3 O S c1ccc(cc1)....
5 2JFX - DGL C5 H9 N O4 C(CC(=O)O)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4B1F - KRH C25 H26 N6 O2 CC(C)CN1c2....
2 2JFY - DGL C5 H9 N O4 C(CC(=O)O)....
3 2JFZ Ki = 5.8 uM 003 C26 H25 N5 O2 CC(C)CN1c2....
4 2W4I ic50 = 0.5 uM VGA C22 H19 N3 O S c1ccc(cc1)....
5 2JFX - DGL C5 H9 N O4 C(CC(=O)O)....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2JFV - FLC C6 H5 O7 C(C(=O)[O-....
2 2JFQ - DGL C5 H9 N O4 C(CC(=O)O)....
3 2DWU - DGL C5 H9 N O4 C(CC(=O)O)....
4 2JFO - DGL C5 H9 N O4 C(CC(=O)O)....
5 2VVT ic50 = 5.8 uM I24 C22 H28 F2 N6 O2 CCCCOc1nc(....
6 2JFP - DGL C5 H9 N O4 C(CC(=O)O)....
7 2OHV Ki = 16 nM NHL C16 H17 N O4 c1ccc2cc(c....
8 1B74 Ki = 50 mM DGN C5 H10 N2 O3 C(CC(=O)N)....
9 1ZUW - DGL C5 H9 N O4 C(CC(=O)O)....
10 2GZM - DGL C5 H9 N O4 C(CC(=O)O)....
11 4B1F - KRH C25 H26 N6 O2 CC(C)CN1c2....
12 2JFY - DGL C5 H9 N O4 C(CC(=O)O)....
13 2JFZ Ki = 5.8 uM 003 C26 H25 N5 O2 CC(C)CN1c2....
14 2W4I ic50 = 0.5 uM VGA C22 H19 N3 O S c1ccc(cc1)....
15 2JFX - DGL C5 H9 N O4 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 003; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 003 1 1
2 KRH 0.697917 0.983333
Ligand no: 2; Ligand: DGL; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 GGL 1 1
2 GLU 1 1
3 DGL 1 1
4 DGN 0.62963 0.821429
5 GLN 0.62963 0.821429
6 ONL 0.586207 0.821429
7 UN1 0.566667 0.96
8 11C 0.566667 0.96
9 HCS 0.555556 0.714286
10 NPI 0.53125 0.923077
11 HGA 0.53125 0.666667
12 HSE 0.518519 0.758621
13 DAB 0.518519 0.666667
14 MEQ 0.515152 0.71875
15 3O3 0.513514 0.727273
16 NVA 0.5 0.740741
17 API 0.5 0.884615
18 DAS 0.481481 0.846154
19 ASP 0.481481 0.846154
20 TNA 0.463415 0.685714
21 DBB 0.461538 0.692308
22 ABA 0.461538 0.692308
23 DSN 0.461538 0.655172
24 SER 0.461538 0.655172
25 RGP 0.459459 0.648649
26 ORN 0.451613 0.689655
27 HOZ 0.451613 0.666667
28 AE5 0.447368 0.727273
29 DCY 0.444444 0.642857
30 C2N 0.444444 0.666667
31 CYS 0.444444 0.642857
32 NLE 0.4375 0.689655
33 2HG 0.433333 0.653846
34 S2G 0.433333 0.653846
35 ASN 0.428571 0.677419
36 26P 0.428571 0.857143
37 3GC 0.425 0.705882
38 DLY 0.424242 0.666667
39 MED 0.424242 0.625
40 MET 0.424242 0.625
41 MSE 0.424242 0.606061
42 BIX 0.418605 0.631579
43 MF3 0.416667 0.625
44 CBH 0.414634 0.774194
45 DHH 0.411765 0.851852
46 LYS 0.411765 0.645161
47 SHR 0.409091 0.774194
48 2NP 0.405405 0.71875
49 AS2 0.4 0.84
50 5OY 0.4 0.648649
51 ONH 0.4 0.611111
52 2JJ 0.4 0.648649
53 LEU 0.4 0.642857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2JFZ; Ligand: DGL; Similar sites found with APoc: 110
This union binding pocket(no: 1) in the query (biounit: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 1SQL GUN None
3 2WTS ALA 1.40845
4 4QEK GLC 1.56863
5 3ROE THM 1.96078
6 5THQ NDP 1.96078
7 4TV1 36M 1.99203
8 4Z7X 3CX 2.10084
9 5LV1 78T 2.35294
10 4C5N ACP 2.35294
11 3ZS7 ATP 2.35294
12 2QEN ADP 2.35294
13 4HBM 0Y7 2.5
14 2WT9 NIO 2.55319
15 5LOG LDP 2.57511
16 2XEM SSV 2.66667
17 4DXJ 0M9 2.7451
18 3UN3 G16 2.7451
19 1SJD NPG 2.7451
20 2B8W ALF 5GP 2.7451
21 4WT2 3UD 2.85714
22 4OAS 2SW 3.125
23 3A51 VDY 3.13725
24 1S20 TLA 3.13725
25 2NPA MMB 3.13725
26 1K7L 544 3.13725
27 2BJ4 OHT 3.1746
28 1TID ATP 3.36134
29 5OLK DTP 3.52941
30 3LXI CAM 3.52941
31 1CZA ADP 3.52941
32 2Q4X HMH 3.61991
33 3QVL 5HY 3.67347
34 2ITM XUL 3.71901
35 5F90 GLA GAL BGC 5VQ 3.84615
36 4GFD 0YB 3.90244
37 3TDC 0EU 3.92157
38 5E70 RCD 3.92157
39 5NCB JZ3 3.92157
40 1KNY KAN 3.95257
41 2WDA L42 4.31373
42 4X6X S74 4.31373
43 3DLS ADP 4.31373
44 2ALG HP6 4.34783
45 2ALG DAO 4.34783
46 1PWB GLC 4.51977
47 3KP6 SAL 4.63576
48 3JU6 ARG 4.70588
49 5TXR PLP 4.70588
50 4TQK NAG 4.70588
51 4NSQ COA 4.73684
52 1E4I NFG 5.09804
53 2J5V RGP 5.09804
54 4R8L ASP 5.09804
55 1ON3 DXX 5.09804
56 4OOE FOM 5.09804
57 2BZ1 TAU 5.10204
58 1NU4 MLA 5.15464
59 3LA3 2FT 5.34979
60 5GQX GLC GLC GLC 5.4902
61 3JYY PPV 5.4902
62 5EE7 5MV 5.4902
63 5EY0 GTP 5.4902
64 4LSJ LSJ 5.4902
65 1EI6 PPF 5.4902
66 3SLS 77D 5.4902
67 5U83 ZN8 5.66038
68 5ICK FEZ 5.67686
69 4WGF HX2 5.85366
70 3II1 BGC 5.88235
71 3X01 AMP 6.27451
72 6FYV 3NG 6.66667
73 2WPW ACO 6.66667
74 4RHE FMN 6.69856
75 3GWN FAD 7.01754
76 4LWU 20U 7.05882
77 5WS9 OXL 7.05882
78 3A06 FOM 7.05882
79 4GCZ FMN 7.05882
80 2WPX ACO 7.05882
81 5LX9 OLB 7.45098
82 5O0J GLC 7.45098
83 1I7L ATP 7.45098
84 5CYV WCA 7.53425
85 5KOR GDP 7.84314
86 6CB2 OLC 8.23529
87 2G50 PYR 8.23529
88 3A9B BGC 9.41177
89 3WFD AXO 9.77778
90 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 9.80392
91 2HIM ASN 9.80392
92 2HIM ASP 9.80392
93 2H7C SIA 9.80392
94 2Y69 CHD 10
95 5X8Q 82R 10.1961
96 3K56 IS3 10.1961
97 2BCG GER 10.6796
98 4JEM C5P 12.9412
99 5W97 CHD 13.0435
100 5ZCO PEK 13.0435
101 3TTN SPD 13.7255
102 2QLX RM4 13.8889
103 2WOR 2AN 14
104 2PR5 FMN 14.3939
105 5IWQ PLP 15.6863
106 5UI2 SUC 16.8627
107 2DX7 CIT 21.4912
108 5HRA DAS 25.5319
109 5B19 TLA 25.8621
110 3PMA SCR 27.5862
Pocket No.: 2; Query (leader) PDB : 2JFZ; Ligand: DGL; Similar sites found with APoc: 38
This union binding pocket(no: 2) in the query (biounit: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
1 3BIB PSF None
2 4NB5 2JT None
3 6BOC RIM None
4 2Z9V PXM 1.96078
5 1M3U KPL 1.96078
6 5M1Z 6LW AHR 1.96078
7 3EWK FAD 2.20264
8 1RYO OXL 2.35294
9 4JX1 CAH 2.7451
10 4JX1 CAM 2.7451
11 2Y24 XYP XYP GCV XYP 2.7451
12 5B0I BOG 2.7451
13 2OI2 DP6 3.13725
14 5E9H MLI 3.52941
15 5E9G GLV 3.52941
16 2F2G HMH 3.61991
17 2JHP GUN 3.92157
18 1H9G COA MYR 4.11523
19 4YSX EPH 4.25532
20 1F1V DHY 4.31373
21 2HFK E4H 4.31373
22 5V3Y 5V8 4.31373
23 5DKK FMN 4.82759
24 3K1X DBX 5.38462
25 1DEK DGP 5.39419
26 4P6X HCY 5.4902
27 1R6N 434 5.6872
28 4RJD TFP 6.06061
29 2CNT COA 6.875
30 3P7N FMN 8.23529
31 4RL4 PPV 9.01961
32 6FS0 E4W 9.17431
33 3VPD CIT 9.80392
34 6FHQ DE5 10.3448
35 1CX4 CMP 10.5882
36 5ZCO CHD 13.0435
37 1TUK PGM 16.4179
38 5MBC FMN 31.3725
Pocket No.: 3; Query (leader) PDB : 2JFZ; Ligand: 003; Similar sites found with APoc: 106
This union binding pocket(no: 3) in the query (biounit: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
1 1SQL GUN None
2 3BIB PSF None
3 1ZEI CRS None
4 4NB5 2JT None
5 6BOC RIM None
6 4QEK GLC 1.56863
7 3ROE THM 1.96078
8 2Z9V PXM 1.96078
9 1M3U KPL 1.96078
10 5M1Z 6LW AHR 1.96078
11 5THQ NDP 1.96078
12 4TV1 36M 1.99203
13 4Z7X 3CX 2.10084
14 3EWK FAD 2.20264
15 5LV1 78T 2.35294
16 1RYO OXL 2.35294
17 4C5N ACP 2.35294
18 4HBM 0Y7 2.5
19 2XEM SSV 2.66667
20 4JX1 CAH 2.7451
21 4JX1 CAM 2.7451
22 2Y24 XYP XYP GCV XYP 2.7451
23 5B0I BOG 2.7451
24 2B8W ALF 5GP 2.7451
25 4WT2 3UD 2.85714
26 4OAS 2SW 3.125
27 1S20 TLA 3.13725
28 2OI2 DP6 3.13725
29 2NPA MMB 3.13725
30 1K7L 544 3.13725
31 1TID ATP 3.36134
32 5E9H MLI 3.52941
33 1CZA ADP 3.52941
34 3LXI CAM 3.52941
35 5E9G GLV 3.52941
36 2Q4X HMH 3.61991
37 2F2G HMH 3.61991
38 3QVL 5HY 3.67347
39 5F90 GLA GAL BGC 5VQ 3.84615
40 4GFD 0YB 3.90244
41 3TDC 0EU 3.92157
42 5E70 RCD 3.92157
43 2JHP GUN 3.92157
44 1KNY KAN 3.95257
45 1H9G COA MYR 4.11523
46 4YSX EPH 4.25532
47 2WDA L42 4.31373
48 1F1V DHY 4.31373
49 2HFK E4H 4.31373
50 5V3Y 5V8 4.31373
51 4X6X S74 4.31373
52 3KP6 SAL 4.63576
53 4NSQ COA 4.73684
54 5DKK FMN 4.82759
55 1E4I NFG 5.09804
56 2J5V RGP 5.09804
57 4OOE FOM 5.09804
58 1ON3 DXX 5.09804
59 2BZ1 TAU 5.10204
60 1NU4 MLA 5.15464
61 3LA3 2FT 5.34979
62 3K1X DBX 5.38462
63 1DEK DGP 5.39419
64 5GQX GLC GLC GLC 5.4902
65 3JYY PPV 5.4902
66 5EE7 5MV 5.4902
67 1EI6 PPF 5.4902
68 4LSJ LSJ 5.4902
69 4P6X HCY 5.4902
70 5U83 ZN8 5.66038
71 5ICK FEZ 5.67686
72 1R6N 434 5.6872
73 4WGF HX2 5.85366
74 4RJD TFP 6.06061
75 3X01 AMP 6.27451
76 2WPW ACO 6.66667
77 4RHE FMN 6.69856
78 2CNT COA 6.875
79 3GWN FAD 7.01754
80 4LWU 20U 7.05882
81 5WS9 OXL 7.05882
82 3A06 FOM 7.05882
83 2WPX ACO 7.05882
84 5LX9 OLB 7.45098
85 6CB2 OLC 8.23529
86 3P7N FMN 8.23529
87 4RL4 PPV 9.01961
88 6FS0 E4W 9.17431
89 3WFD AXO 9.77778
90 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 9.80392
91 2H7C SIA 9.80392
92 3VPD CIT 9.80392
93 2Y69 CHD 10
94 6FHQ DE5 10.3448
95 1CX4 CMP 10.5882
96 5W97 CHD 13.0435
97 5ZCO CHD 13.0435
98 3TTN SPD 13.7255
99 5IWQ PLP 15.6863
100 1TUK PGM 16.4179
101 5UI2 SUC 16.8627
102 2DX7 CIT 21.4912
103 5HRA DAS 25.5319
104 5B19 TLA 25.8621
105 3PMA SCR 27.5862
106 5MBC FMN 31.3725
Pocket No.: 4; Query (leader) PDB : 2JFZ; Ligand: 003; Similar sites found with APoc: 42
This union binding pocket(no: 4) in the query (biounit: 2jfz.bio1) has 56 residues
No: Leader PDB Ligand Sequence Similarity
1 2WTS ALA 1.40845
2 5JH2 A2P 1.96078
3 3ZS7 ATP 2.35294
4 2WT9 NIO 2.55319
5 5LOG LDP 2.57511
6 4DXJ 0M9 2.7451
7 1SJD NPG 2.7451
8 5LD5 NAD 2.7451
9 3SP6 IL2 3.13725
10 2BJ4 OHT 3.1746
11 5OLK DTP 3.52941
12 6EXS C3H 3.52941
13 2ITM XUL 3.71901
14 1YBU APC 3.80435
15 5NCB JZ3 3.92157
16 1PWB GLC 4.51977
17 3JU6 ARG 4.70588
18 5TXR PLP 4.70588
19 4TQK NAG 4.70588
20 4R8L ASP 5.09804
21 2OWZ CIT 5.4902
22 5EY0 GTP 5.4902
23 3II1 BGC 5.88235
24 3A72 AHR AHR 5.88235
25 6FYV 3NG 6.66667
26 3ZGE ASP 6.66667
27 4GCZ FMN 7.05882
28 1I7L ATP 7.45098
29 5CYV WCA 7.53425
30 5KOR GDP 7.84314
31 2G50 PYR 8.23529
32 3HCH RSM 8.90411
33 3A9B BGC 9.41177
34 2HIM ASN 9.80392
35 5X8Q 82R 10.1961
36 2BCG GER 10.6796
37 3R51 MMA 11.25
38 4JEM C5P 12.9412
39 5Z84 CHD 13.0435
40 5ZCO PEK 13.0435
41 2QLX RM4 13.8889
42 2WOR 2AN 14
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