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 (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2JFV - FLC C6 H5 O7 C(C(=O)[O-....
2 2JFQ - DGL C5 H9 N O4 C(CC(=O)O)....
3 2VVT ic50 = 5.8 uM I24 C22 H28 F2 N6 O2 CCCCOc1nc(....
4 2JFP - DGL C5 H9 N O4 C(CC(=O)O)....
5 1B74 Ki = 50 mM DGN C5 H10 N2 O3 C(CC(=O)N)....
6 1ZUW - DGL C5 H9 N O4 C(CC(=O)O)....
7 2GZM - DGL C5 H9 N O4 C(CC(=O)O)....
8 4B1F - KRH C25 H26 N6 O2 CC(C)CN1c2....
9 2JFY - DGL C5 H9 N O4 C(CC(=O)O)....
10 2JFZ Ki = 5.8 uM 003 C26 H25 N5 O2 CC(C)CN1c2....
11 2W4I ic50 = 0.5 uM VGA C22 H19 N3 O S c1ccc(cc1)....
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 GLU 1 1
2 DGL 1 1
3 GGL 1 1
4 GLN 0.62963 0.821429
5 DGN 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 HGA 0.53125 0.666667
11 NPI 0.53125 0.923077
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 API 0.5 0.884615
17 NVA 0.5 0.740741
18 ASP 0.481481 0.846154
19 DAS 0.481481 0.846154
20 TNA 0.463415 0.685714
21 ABA 0.461538 0.692308
22 DSN 0.461538 0.655172
23 DBB 0.461538 0.692308
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 CYS 0.444444 0.642857
31 C2N 0.444444 0.666667
32 NLE 0.4375 0.689655
33 S2G 0.433333 0.653846
34 2HG 0.433333 0.653846
35 ASN 0.428571 0.677419
36 26P 0.428571 0.857143
37 3GC 0.425 0.705882
38 MET 0.424242 0.625
39 MSE 0.424242 0.606061
40 DLY 0.424242 0.666667
41 MED 0.424242 0.625
42 BIX 0.418605 0.631579
43 MF3 0.416667 0.625
44 CBH 0.414634 0.774194
45 LYS 0.411765 0.645161
46 DHH 0.411765 0.851852
47 SHR 0.409091 0.774194
48 2NP 0.405405 0.71875
49 LEU 0.4 0.642857
50 5OY 0.4 0.648649
51 AS2 0.4 0.84
52 2JJ 0.4 0.648649
53 ONH 0.4 0.611111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2JFZ; Ligand: DGL; Similar sites found: 59
This union binding pocket(no: 1) in the query (biounit: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SQL GUN 0.04272 0.42495 None
2 2WTS ALA 0.005343 0.40661 1.40845
3 4QEK GLC 0.03652 0.40357 1.56863
4 4Z7X 3CX 0.02696 0.4364 2.10084
5 4HBM 0Y7 0.01747 0.42705 2.5
6 2WT9 NIO 0.02846 0.43547 2.55319
7 5LOG LDP 0.03147 0.44274 2.57511
8 2XEM SSV 0.01693 0.43861 2.66667
9 5XVK 8GC 0.02561 0.43771 2.7451
10 3UN3 G16 0.009223 0.414 2.7451
11 2B8W ALF 5GP 0.02304 0.40428 2.7451
12 4WT2 3UD 0.007142 0.41701 2.85714
13 4OAS 2SW 0.01948 0.42799 3.125
14 3A51 VDY 0.03354 0.41254 3.13725
15 2NPA MMB 0.03135 0.40297 3.13725
16 1K7L 544 0.02526 0.4001 3.13725
17 1TID ATP 0.04 0.40572 3.36134
18 3LXI CAM 0.02182 0.44113 3.52941
19 1CZA ADP 0.03433 0.42699 3.52941
20 2Q4X HMH 0.02884 0.43519 3.61991
21 2ITM XUL 0.03515 0.41697 3.71901
22 5F90 GLA GAL BGC 5VQ 0.04778 0.40996 3.84615
23 4GFD 0YB 0.02102 0.4061 3.90244
24 3TDC 0EU 0.0014 0.51542 3.92157
25 5E70 RCD 0.0234 0.44708 3.92157
26 1KNY KAN 0.02498 0.43591 3.95257
27 2WDA L42 0.04978 0.42201 4.31373
28 4X6X S74 0.01463 0.41867 4.31373
29 2ALG HP6 0.03502 0.40068 4.34783
30 2ALG DAO 0.03502 0.40068 4.34783
31 3JU6 ARG 0.03802 0.42054 4.70588
32 4NSQ COA 0.03917 0.40618 4.73684
33 2J5V RGP 0.0486 0.42585 5.09804
34 1ON3 DXX 0.04038 0.42142 5.09804
35 4OOE FOM 0.02683 0.42072 5.09804
36 3LA3 2FT 0.04535 0.42293 5.34979
37 5GQX GLC GLC GLC 0.01518 0.46524 5.4902
38 5EE7 5MV 0.04528 0.42289 5.4902
39 5EY0 GTP 0.0415 0.41731 5.4902
40 3SLS 77D 0.04332 0.40978 5.4902
41 5U83 ZN8 0.03528 0.42879 5.66038
42 3II1 BGC 0.0285 0.42416 5.88235
43 2WPW ACO 0.0494 0.40384 6.66667
44 4LWU 20U 0.01258 0.43786 7.05882
45 4GCZ FMN 0.03517 0.40577 7.05882
46 2WPX ACO 0.04509 0.40308 7.05882
47 5KOR GDP 0.03089 0.40586 7.84314
48 3A9B BGC 0.03956 0.42207 9.41177
49 3WFD AXO 0.004085 0.42778 9.77778
50 2H7C SIA 0.04032 0.41975 9.80392
51 5X8Q 82R 0.0278 0.41082 10.1961
52 3K56 IS3 0.04372 0.40957 10.1961
53 3TTN SPD 0.0252 0.43661 13.7255
54 2QLX RM4 0.04043 0.41783 13.8889
55 5IWQ PLP 0.006893 0.45547 15.6863
56 2DX7 CIT 0.00003396 0.57067 21.4912
57 5HRA DAS 0.0001808 0.53896 25.5319
58 5B19 TLA 0.000003348 0.64723 25.8621
59 3PMA SCR 0.03997 0.41231 27.5862
Pocket No.: 2; Query (leader) PDB : 2JFZ; Ligand: DGL; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2JFZ; Ligand: 003; Similar sites found: 61
This union binding pocket(no: 3) in the query (biounit: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SQL GUN 0.0278 0.43721 None
2 3BIB PSF 0.02719 0.43587 None
3 4NB5 2JT 0.01177 0.42915 None
4 4QEK GLC 0.03917 0.40357 1.56863
5 5M1Z 6LW AHR 0.04272 0.40428 1.96078
6 4Z7X 3CX 0.03904 0.42756 2.10084
7 1F8I SIN 0.02184 0.44073 2.35294
8 1RYO OXL 0.03832 0.41396 2.35294
9 4HBM 0Y7 0.01926 0.42169 2.5
10 2XEM SSV 0.01509 0.44131 2.66667
11 5XVK 8GC 0.02676 0.43618 2.7451
12 4JX1 CAH 0.03331 0.42541 2.7451
13 4JX1 CAM 0.03935 0.42198 2.7451
14 2Y24 XYP XYP GCV XYP 0.04665 0.42179 2.7451
15 2B8W ALF 5GP 0.02556 0.40222 2.7451
16 4WT2 3UD 0.006167 0.41973 2.85714
17 4OAS 2SW 0.0165 0.43174 3.125
18 2NPA MMB 0.02591 0.40691 3.13725
19 1K7L 544 0.01981 0.40252 3.13725
20 1TID ATP 0.03253 0.41026 3.36134
21 5E9H MLI 0.02391 0.43984 3.52941
22 1CZA ADP 0.03567 0.42608 3.52941
23 3LXI CAM 0.0489 0.4202 3.52941
24 2Q4X HMH 0.02778 0.43619 3.61991
25 2F2G HMH 0.03871 0.42228 3.61991
26 5F90 GLA GAL BGC 5VQ 0.04881 0.4095 3.84615
27 4GFD 0YB 0.01902 0.40809 3.90244
28 3TDC 0EU 0.001569 0.5048 3.92157
29 5E70 RCD 0.0234 0.44708 3.92157
30 2JHP GUN 0.03271 0.41506 3.92157
31 1KNY KAN 0.03316 0.42542 3.95257
32 4YSX EPH 0.03512 0.40315 4.25532
33 2WDA L42 0.03051 0.43555 4.31373
34 4X6X S74 0.0194 0.41287 4.31373
35 5DKK FMN 0.03496 0.4059 4.82759
36 2J5V RGP 0.04793 0.42618 5.09804
37 4OOE FOM 0.02474 0.42256 5.09804
38 1ON3 DXX 0.04002 0.42171 5.09804
39 3LA3 2FT 0.03902 0.4268 5.34979
40 3JUT GTQ 0.01534 0.41313 5.38462
41 1DEK DGP 0.02784 0.41079 5.39419
42 5GQX GLC GLC GLC 0.01431 0.4608 5.4902
43 3JYY PPV 0.03051 0.43231 5.4902
44 5EE7 5MV 0.02998 0.43128 5.4902
45 5U83 ZN8 0.03812 0.42685 5.66038
46 1R6N 434 0.04772 0.42101 5.6872
47 2WPW ACO 0.04368 0.40661 6.66667
48 2CNT COA 0.02075 0.40636 6.875
49 4LWU 20U 0.009925 0.44322 7.05882
50 2WPX ACO 0.04555 0.40286 7.05882
51 3P7N FMN 0.02046 0.41738 8.23529
52 5MES 7LT 0.04766 0.4107 8.64198
53 4RL4 PPV 0.047 0.41138 9.01961
54 3WFD AXO 0.004085 0.42778 9.77778
55 2H7C SIA 0.04143 0.4192 9.80392
56 3TTN SPD 0.02515 0.43666 13.7255
57 2DX7 CIT 0.00002857 0.57455 21.4912
58 5HRA DAS 0.0001716 0.54015 25.5319
59 5B19 TLA 0.000003548 0.64583 25.8621
60 3PMA SCR 0.03682 0.4149 27.5862
61 5MBC FMN 0.04957 0.40377 31.3725
Pocket No.: 4; Query (leader) PDB : 2JFZ; Ligand: 003; 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: 2jfz.bio1) has 56 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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