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Receptor
PDB id Resolution Class Description Source Keywords
2JFQ 2.15 Å EC: 5.1.1.3 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS GLUTAMATE RACEMAS COMPLEX WITH D- GLUTAMATE STAPHYLOCOCCUS AUREUS CELL WALL ISOMERASE CELL SHAPE GLUTAMATE RACEMASE PEPTIDSYNTHESIS PEPTIDOGLYCAN BIOSYNTHESIS
Ref.: EXPLOITATION OF STRUCTURAL AND REGULATORY DIVERSITY GLUTAMATE RACEMASES NATURE V. 447 817 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DGL A:1267;
B:1267;
Valid;
Valid;
none;
none;
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147.129 C5 H9 N O4 C(CC(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2JFQ 2.15 Å EC: 5.1.1.3 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS GLUTAMATE RACEMAS COMPLEX WITH D- GLUTAMATE STAPHYLOCOCCUS AUREUS CELL WALL ISOMERASE CELL SHAPE GLUTAMATE RACEMASE PEPTIDSYNTHESIS PEPTIDOGLYCAN BIOSYNTHESIS
Ref.: EXPLOITATION OF STRUCTURAL AND REGULATORY DIVERSITY GLUTAMATE RACEMASES NATURE V. 447 817 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2JFQ - DGL C5 H9 N O4 C(CC(=O)O)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2JFQ - 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: 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 : 2JFQ; Ligand: DGL; Similar sites found with APoc: 64
This union binding pocket(no: 1) in the query (biounit: 2jfq.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1OGD RIP None
2 6AYI C3G None
3 1X87 NAD 1.74825
4 5NCB JZ3 1.74825
5 2H7C SIA 2.0979
6 1USF NAP 2.24719
7 1USF FMN 2.24719
8 6CI9 F3V 2.3166
9 3FXU TSU 2.44755
10 2WK9 PLP 2.44755
11 2WK9 PLG 2.44755
12 12AS AMP 2.7972
13 4R8L ASP 2.7972
14 5F52 ASP 2.7972
15 2Q0L FAD 2.7972
16 5DNC ASN 2.7972
17 5LV1 78T 2.85714
18 2WKV COA 3.14685
19 3IT6 ORN 3.51759
20 2BZ1 TAU 4.08163
21 1L5J TRA 4.1958
22 1RYO OXL 4.1958
23 4OWK NGA 4.34783
24 5TV6 PML 4.58333
25 5G5G MCN 4.80349
26 2JK0 ASP 4.8951
27 1RDL MMA 5.30973
28 3HGM ATP 5.44218
29 2IVF MGD 5.59441
30 1F8G NAD 5.59441
31 6G1P CIT 5.94406
32 6HQD SRT 5.94406
33 2RCA GLY 5.94406
34 4R0M FA5 5.94406
35 2IVN ANP 6.29371
36 5X7Q GLC GLC GLC GLC 6.29371
37 1M2X MCO 6.72646
38 3X0V FAD 6.99301
39 5EIB GTP 7.34266
40 5ITZ GDP 7.34266
41 3GFS FMN 7.47126
42 3IP8 B85 7.66129
43 1ZUA TOL 7.69231
44 1ZUA NAP 7.69231
45 6BWL NAD 8.04196
46 2PHW MAN MAN 8.33333
47 2PHR MAN MAN 8.33333
48 2GND MAN MMA 8.33333
49 2PHF MAN MAN 8.33333
50 1Q8P MAN MMA 8.33333
51 4XJ7 ADE 9.3633
52 2QTR NXX 9.52381
53 2RIF AMP 9.92908
54 4POO SAM 10
55 1BCJ NGA 10.3896
56 5B48 TDN 11.4754
57 2HIM ASN 11.8881
58 5XFV FMN 12.2378
59 6FHQ DE5 13.7931
60 5B19 TLA 24.1379
61 5HRA DAS 25.1748
62 5EYK 5U5 27.1186
63 3LA3 2FT 30.8642
64 2DX7 CIT 32.4561
Pocket No.: 2; Query (leader) PDB : 2JFQ; Ligand: DGL; Similar sites found with APoc: 32
This union binding pocket(no: 2) in the query (biounit: 2jfq.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 3C3N FMN 2.0979
2 3AYI FAD 2.44755
3 3AYI HCI 2.44755
4 2CE7 ADP 2.7972
5 1NVM NAD 2.7972
6 4IXH IMP 3.14685
7 1KOL NAD 3.26633
8 1PWB GLC 3.38983
9 3BNK FMN 3.57143
10 2WT9 NIO 3.82979
11 3VWX GSH 4.05405
12 4B7X NAP 4.54545
13 3N5O GSH 5.10638
14 1RM6 FAD 5.24476
15 6AM8 PLT 5.59441
16 5X7Q GLC GLC GLC 6.29371
17 5W3K 9TY 6.29371
18 1FUI FOC 6.64336
19 4JAW NGT GAL 7.34266
20 4D9C PMP 7.34266
21 1JZN BGC GAL 7.40741
22 2IVD FAD 7.53138
23 3B2Q ATP 7.69231
24 5YB7 FAD 8.04196
25 5YB7 ORN 8.04196
26 4D5G TPP 9.44056
27 4D5G FAD 9.44056
28 1J0D 5PA 9.44056
29 3JYY PPV 9.79021
30 4WZH FMN 10.1399
31 5M7S NHT 11.8881
32 2V6K TGG 14.486
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