Receptor
PDB id Resolution Class Description Source Keywords
3deq 2.1 Å EC: 5.-.-.- CRYSTAL STRUCTURE OF DIPEPTIDE EPIMERASE FROM THERMOTOGA MARITIMA COMPLEXED WITH L-ALA-L-LEU 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 LEU A:411;
B:411;
C:411;
D:411;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
201.246 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...
View in 3D viewer
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 LEU; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA LEU 1 1
2 GLY LEU 0.538462 0.823529
3 ALA GLN 0.536585 0.764706
4 LEU LEU LEU 0.533333 0.90625
5 ALA LEU ALA LEU 0.489796 0.90625
6 ALA LYS 0.488889 0.702703
7 SER SER ARG THR ARG ARG GLU GLU GLN LEU 0.481481 0.805556
8 PHE LEU 0.480769 0.878788
9 ALA ALA 0.459459 0.827586
10 GLY THR LEU SER ASN ARG ALA SER LYS LEU 0.453125 0.659091
11 GLU ASP LEU 0.45283 0.805556
12 ALA PHE 0.44898 0.8125
13 ALA ARG 0.44898 0.604651
14 SER PRO SER ILE 0.44898 0.7
15 LEU GLU 0.446809 0.878788
16 LYS ASN LEU 0.438596 0.674419
17 LEU LYS 0.403846 0.783784
Similar Ligands (3D)
Ligand no: 1; Ligand: ALA LEU; Similar ligands found: 88
No: Ligand Similarity coefficient
1 NQM 0.9587
2 GLY ASP 0.9420
3 PRO LEU 0.9292
4 CDT 0.9270
5 0GY 0.9203
6 HCA 0.9176
7 KFN 0.9152
8 FLC 0.9150
9 NLQ 0.9112
10 C4L 0.9104
11 CIT 0.9100
12 DG2 0.9098
13 ALA GLU 0.9095
14 GLY MET 0.9095
15 ALA ZGL 0.9086
16 NLG 0.9076
17 8VE 0.9068
18 G01 0.9064
19 1AL 0.9053
20 AOR 0.9050
21 SER THR 0.9040
22 6XI 0.9039
23 7QD 0.9039
24 0FA 0.9025
25 ALA DGL 0.9009
26 TRA 0.8998
27 4WK 0.8983
28 AN0 0.8974
29 EKN 0.8974
30 AM1 0.8967
31 PAL 0.8962
32 HCT 0.8961
33 HJ7 0.8956
34 CCB 0.8955
35 2C0 0.8954
36 JAA 0.8951
37 AME 0.8947
38 NIG 0.8945
39 P4B 0.8932
40 CE2 0.8916
41 NCD 0.8914
42 AQK 0.8912
43 87L 0.8902
44 AIN 0.8883
45 GV9 0.8881
46 TRC 0.8875
47 KDO 0.8872
48 692 0.8870
49 8VN 0.8865
50 ICT 0.8863
51 F12 0.8851
52 G88 0.8849
53 AVO 0.8829
54 3MF 0.8822
55 V6F 0.8822
56 1FF 0.8813
57 2BQ 0.8809
58 1PL 0.8796
59 CIL 0.8786
60 P8D 0.8774
61 OTD 0.8767
62 U1K 0.8767
63 AVI 0.8766
64 NFQ 0.8758
65 2D3 0.8751
66 7A2 0.8743
67 ATH 0.8735
68 XQB 0.8718
69 XQK 0.8714
70 KAI 0.8711
71 S2T 0.8707
72 DY8 0.8699
73 512 0.8679
74 791 0.8674
75 M5N 0.8664
76 BRR 0.8661
77 A9O 0.8660
78 NZ3 0.8660
79 DXG 0.8651
80 XH2 0.8631
81 PRZ 0.8626
82 AQQ 0.8614
83 OKM 0.8610
84 S7B 0.8609
85 7A3 0.8596
86 7WR 0.8593
87 256 0.8584
88 VPR 0.8552
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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