Receptor
PDB id Resolution Class Description Source Keywords
3DES 2.3 Å EC: 5.-.-.- CRYSTAL STRUCTURE OF DIPEPTIDE EPIMERASE FROM THERMOTOGA MARITIMA COMPLEXED WITH L-ALA-L-PHE DIPEPTIDE THERMOTOGA MARITIMA MSB8 DIPEPTIDE EPIMERASE THERMOTOGA MARITIMA ENZYMATIC FUNCTION ISOMERASE
Ref.: DISCOVERY OF A DIPEPTIDE EPIMERASE ENZYMATIC FUNCTION GUIDED BY HOMOLOGY MODELING AND VIRTUAL SCREENING. STRUCTURE V. 16 1668 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA PHE A:411;
B:411;
C:411;
D:411;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
235.263 n/a O=C([...
MG A:401;
B:401;
C:401;
D:401;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DER 1.9 Å EC: 5.-.-.- CRYSTAL STRUCTURE OF DIPEPTIDE EPIMERASE FROM THERMOTOGA MARITIMA COMPLEXED WITH L-ALA-L-LYS DIPEPTIDE THERMOTOGA MARITIMA MSB8 DIPEPTIDE EPIMERASE THERMOTOGA MARITIMA ENZYMATIC FUNCTION ISOMERASE
Ref.: DISCOVERY OF A DIPEPTIDE EPIMERASE ENZYMATIC FUNCTION GUIDED BY HOMOLOGY MODELING AND VIRTUAL SCREENING. STRUCTURE V. 16 1668 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 30 families.
1 3DES - ALA PHE n/a n/a
2 3DER - ALA LYS n/a n/a
3 3DEQ - ALA LEU n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 3DES - ALA PHE n/a n/a
2 3DER - ALA LYS n/a n/a
3 3DEQ - ALA LEU n/a n/a
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 1TKK - ALA GLU n/a n/a
2 3DES - ALA PHE n/a n/a
3 3DER - ALA LYS n/a n/a
4 3DEQ - ALA LEU n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ALA PHE; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA PHE 1 1
2 ASP PHE 0.653846 0.848485
3 ACE LEU PHE 0.607143 0.777778
4 ALA LEU ASP LEU PHE 0.580645 0.783784
5 PHE LEU 0.54386 0.878788
6 GLU THR LEU GLU ASP SER VAL PHE 0.521739 0.674419
7 PHE ALA 0.509091 0.966667
8 ACE SER LEU ASN PHE 0.479452 0.630435
9 ALA GLU THR PHE 0.478873 0.707317
10 VAL TYR 0.474576 0.783784
11 THR ASN GLU PHE ALA PHE 0.473684 0.725
12 TYR GLN PHE 0.464789 0.666667
13 ING 0.461538 0.675676
14 BES 0.460317 0.658537
15 ALA GLN 0.45098 0.764706
16 ALA LEU 0.44898 0.8125
17 PHE ALA GLN 0.447761 0.852941
18 ACE MET GLU GLU VAL PHE 0.443038 0.622222
19 ASP ALA ASP GLU GLU ASP PHE 0.441558 0.725
20 THR ASN GLU PHE TYR PHE 0.435897 0.622222
21 THR LEU MET THR GLY GLN LEU GLY LEU PHE 0.426829 0.690476
22 CYS ASP PTR ALA ASN PHE LYS 0.426667 0.674419
23 LYS LYS SER LYS THR LYS CYS VAL ILE PHE 0.423529 0.630435
24 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.423529 0.644444
25 LEU SER PRO ASP SER PHE LEU ASN ASP 0.42029 0.642857
26 ALA LYS 0.418182 0.702703
27 SFK 0.416667 0.657895
28 BWX 0.409091 0.675676
29 ALA PHE THR 0.409091 0.777778
30 OIR 0.409091 0.72973
31 NFA 0.408163 0.733333
32 ASP PHE SER ILE 0.407895 0.659091
33 ASP ASN ARG LEU GLY LEU VAL TYR TRP PHE 0.404494 0.604167
Similar Ligands (3D)
Ligand no: 1; Ligand: ALA PHE; Similar ligands found: 73
No: Ligand Similarity coefficient
1 LHY 0.9596
2 GLY PHE 0.9548
3 GLY TYR 0.9383
4 8V0 0.9341
5 ACE PHE 0.9288
6 BZS 0.9248
7 CXA 0.9234
8 3NF 0.9166
9 JGM 0.9164
10 BPX 0.9144
11 CPM 0.9125
12 DY8 0.9086
13 BZM 0.9061
14 9F5 0.9028
15 SQY 0.9000
16 L1T 0.8988
17 536 0.8950
18 23N 0.8949
19 BN1 0.8931
20 0MB 0.8917
21 90J 0.8907
22 TH4 0.8900
23 MS8 0.8899
24 SFY 0.8846
25 ALA DGL 0.8845
26 AVO 0.8843
27 GG5 0.8832
28 UN3 0.8823
29 2E5 0.8820
30 7QD 0.8803
31 RK4 0.8803
32 ALA GLU 0.8788
33 0QR 0.8781
34 YTZ 0.8777
35 S46 0.8777
36 IM4 0.8774
37 IRN 0.8770
38 29B 0.8752
39 SNJ 0.8750
40 Q8D 0.8748
41 25O 0.8745
42 JI2 0.8742
43 Q8G 0.8734
44 PRE 0.8728
45 ISJ 0.8718
46 EV2 0.8717
47 RDY 0.8715
48 9DX 0.8708
49 7NU 0.8695
50 5KN 0.8693
51 UM3 0.8687
52 DI9 0.8685
53 NAL 0.8680
54 6FR 0.8641
55 0OP 0.8633
56 VAL LYS 0.8631
57 N1Y 0.8624
58 AE5 0.8617
59 8CC 0.8617
60 LZ5 0.8615
61 JR2 0.8603
62 FOQ 0.8598
63 FZ0 0.8588
64 60L 0.8585
65 2E4 0.8577
66 W8G 0.8569
67 1BY 0.8565
68 6DQ 0.8560
69 6MW 0.8555
70 1ZC 0.8555
71 IB3 0.8548
72 Q9P 0.8546
73 JGY 0.8511
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DER; Ligand: ALA LYS; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 3der.bio3) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3DGB MUC 38.5507
2 3DGB MUC 38.5507
Pocket No.: 2; Query (leader) PDB : 3DER; Ligand: ALA LYS; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 3der.bio3) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 3DGB MUC 38.5507
2 3DGB MUC 38.5507
Pocket No.: 3; Query (leader) PDB : 3DER; Ligand: ALA LYS; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3der.bio3) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3DER; Ligand: ALA LYS; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 3der.bio3) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3DGB MUC 38.5507
2 3DGB MUC 38.5507
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