Receptor
PDB id Resolution Class Description Source Keywords
1KO0 2.2 Å EC: 4.1.1.20 CRYSTAL STRUCTURE OF A D,L-LYSINE COMPLEX OF DIAMINOPIMELATE DECARBOXYLASE ESCHERICHIA COLI PYRIDOXAL-5-prime -PHOSPHATE DIAMINOPIMELATE LYSINE PLP TIM-BALYASE
Ref.: DIAMINOPIMELATE DECARBOXYLASE USES A VERSATILE ACTI FOR STEREOSPECIFIC DECARBOXYLATION TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DLY A:542;
Valid;
none;
submit data
146.188 C6 H14 N2 O2 C(CCN...
LYS A:541;
Valid;
none;
submit data
147.195 C6 H15 N2 O2 C(CC[...
PLP A:540;
Part of Protein;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KO0 2.2 Å EC: 4.1.1.20 CRYSTAL STRUCTURE OF A D,L-LYSINE COMPLEX OF DIAMINOPIMELATE DECARBOXYLASE ESCHERICHIA COLI PYRIDOXAL-5-prime -PHOSPHATE DIAMINOPIMELATE LYSINE PLP TIM-BALYASE
Ref.: DIAMINOPIMELATE DECARBOXYLASE USES A VERSATILE ACTI FOR STEREOSPECIFIC DECARBOXYLATION TO BE PUBLISHED
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1KO0 - LYS C6 H15 N2 O2 C(CC[NH3+]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1KO0 - LYS C6 H15 N2 O2 C(CC[NH3+]....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1KO0 - LYS C6 H15 N2 O2 C(CC[NH3+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DLY; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 DLY 1 1
2 ORN 0.714286 0.961538
3 2YG 0.609756 0.742857
4 API 0.607143 0.758621
5 LYS 0.59375 0.962963
6 DHH 0.59375 0.733333
7 2YJ 0.585366 0.742857
8 NPI 0.575758 0.733333
9 DAB 0.571429 0.857143
10 NLE 0.53125 0.7
11 MLY 0.527778 0.657895
12 MLZ 0.527778 0.787879
13 5CT 0.52381 0.764706
14 11C 0.515152 0.7
15 UN1 0.515152 0.7
16 0TF 0.511628 0.742857
17 ALY 0.487179 0.764706
18 HRG 0.487179 0.787879
19 ONH 0.485714 0.714286
20 NOT 0.475 0.735294
21 EXY 0.475 0.638889
22 26P 0.472222 0.636364
23 6CL 0.472222 0.733333
24 HSE 0.466667 0.709677
25 2YH 0.465116 0.735294
26 2RA 0.464286 0.758621
27 CIR 0.459459 0.714286
28 HCS 0.451613 0.785714
29 NVA 0.451613 0.689655
30 2NP 0.447368 0.628571
31 ARG 0.447368 0.735294
32 DAR 0.447368 0.735294
33 LBY 0.434783 0.619048
34 REZ 0.431818 0.638889
35 MSE 0.428571 0.617647
36 DGL 0.424242 0.666667
37 GLU 0.424242 0.666667
38 GGL 0.424242 0.666667
39 DGN 0.424242 0.65625
40 GLN 0.424242 0.65625
41 ILO 0.414634 0.735294
42 DSN 0.413793 0.666667
43 ABA 0.413793 0.642857
44 SER 0.413793 0.666667
45 DBB 0.413793 0.642857
46 SHR 0.413043 0.83871
47 DDK 0.410256 0.709677
48 DDW 0.410256 0.733333
49 ONL 0.4 0.606061
50 CYS 0.4 0.714286
51 C2N 0.4 0.678571
52 DCY 0.4 0.714286
Ligand no: 2; Ligand: LYS; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS 1 1
2 LYN 0.612903 0.741935
3 DLY 0.59375 0.962963
4 API 0.586207 0.733333
5 DHH 0.575758 0.709677
6 NPI 0.558824 0.709677
7 ORN 0.53125 0.925926
8 M3L 0.527778 0.604651
9 NLE 0.515152 0.677419
10 6HN 0.513514 0.604651
11 MLY 0.513514 0.641026
12 MLZ 0.513514 0.764706
13 ALY 0.512821 0.742857
14 11C 0.5 0.677419
15 6CL 0.5 0.766667
16 UN1 0.5 0.677419
17 HRG 0.475 0.764706
18 ONH 0.472222 0.694444
19 EXY 0.463415 0.621622
20 NOT 0.463415 0.764706
21 26P 0.459459 0.617647
22 HSE 0.451613 0.6875
23 DAB 0.451613 0.827586
24 CIR 0.447368 0.694444
25 HCS 0.4375 0.758621
26 NVA 0.4375 0.666667
27 2NP 0.435897 0.611111
28 ARG 0.435897 0.764706
29 DAR 0.435897 0.764706
30 REZ 0.422222 0.621622
31 5CT 0.413043 0.742857
32 DGL 0.411765 0.645161
33 GGL 0.411765 0.645161
34 DGN 0.411765 0.636364
35 GLN 0.411765 0.636364
36 GLU 0.411765 0.645161
37 ILO 0.404762 0.714286
38 SHR 0.404255 0.8125
39 0TF 0.404255 0.722222
40 2RA 0.4 0.733333
41 ABA 0.4 0.62069
42 DSN 0.4 0.645161
43 SER 0.4 0.645161
44 DBB 0.4 0.62069
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KO0; Ligand: LYS; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 1ko0.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4LNL PLG 0.005868 0.42882 1.8018
2 4LNL 2BO 0.01037 0.41927 1.8018
3 4LNL 2BK 0.01037 0.41927 1.8018
4 4GYW UDP 0.02769 0.41916 1.88235
5 1R27 MGD 0.009043 0.44839 2.11765
6 2ZWS PLM 0.008486 0.42261 2.11765
7 3OZG SSI 0.02517 0.40091 2.4
8 3E5P PPI 0.002851 0.44714 2.42588
9 1HFA PIO 0.00001628 0.60004 2.76817
10 1HEX NAD 0.01343 0.43019 2.89855
11 2NW9 FT6 0.002372 0.4334 2.94118
12 1FP1 HCC 0.0237 0.40588 3.49462
13 1Z44 NPO 0.005736 0.43122 3.5503
14 1R37 NAD 0.04563 0.41009 3.7464
15 3PJU C2E 0.01694 0.42382 4.01606
16 2WGC SIA GAL BGC 0.003451 0.44238 4.09357
17 1WGC SIA GAL BGC 0.01235 0.40555 4.09357
18 1C1L GAL BGC 0.003449 0.40244 4.37956
19 3BS8 PMP 0.01263 0.41091 4.70588
20 3AHC TPP 0.03314 0.4129 4.94118
21 3IHB TRS 0.01639 0.43215 5.41176
22 2DKH FAD 0.03805 0.41314 5.41176
23 2C31 ADP 0.02398 0.44909 5.64706
24 2C31 TZD 0.02453 0.44909 5.64706
25 4M5P MLA 0.01557 0.40069 6.38821
26 1Y1A GSH 0.003387 0.44653 6.55738
27 3S9K CIT 0.004777 0.43681 6.77966
28 1SBZ FMN 0.03572 0.41348 7.1066
29 3PNL ADP 0.01873 0.41584 7.28291
30 1NOW IFG 0.002883 0.42957 8
31 2D37 FMN 0.004208 0.4539 8.52273
32 2BZ1 TAU 0.01993 0.40376 8.67347
33 1SS4 CIT 0.01611 0.44406 13.0719
34 2YD6 FLC 0.04726 0.40283 13.2075
35 2WQP WQP 0.01557 0.42565 15.7593
36 3N2O AG2 0.0006094 0.42486 19.5294
37 1T0S BML 0.003708 0.4137 19.7674
Pocket No.: 2; Query (leader) PDB : 1KO0; Ligand: DLY; Similar sites found: 27
This union binding pocket(no: 2) in the query (biounit: 1ko0.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4G1V FAD 0.03917 0.40021 1.50376
2 3E5P PPI 0.01975 0.42388 2.42588
3 3TKA CTN 0.02427 0.40723 2.59366
4 1HFA PIO 0.00002863 0.59493 2.76817
5 1JA9 NDP 0.04561 0.42731 2.91971
6 4RJK PYR 0.01874 0.40872 3.05882
7 1FP1 HCC 0.009878 0.41775 3.49462
8 1Z42 HBA 0.002197 0.46519 3.5503
9 2VQ5 LDP 0.007323 0.412 3.9801
10 3FPZ AHZ 0.006145 0.47818 3.98773
11 2WGC SIA GAL BGC 0.003411 0.44663 4.09357
12 1WGC SIA GAL BGC 0.01469 0.40555 4.09357
13 2F01 BTN 0.01859 0.44638 4.72441
14 3AHC TPP 0.01934 0.41885 4.94118
15 4RNV FMN 0.01318 0.40149 4.94118
16 1YOA FMN 0.001545 0.4642 5.03145
17 3IHB TRS 0.00004024 0.57165 5.41176
18 4LWA Q13 0.03273 0.41691 5.88235
19 1TDF NAP 0.02485 0.44253 6.32911
20 4M5P MLA 0.01848 0.40069 6.38821
21 3C1O NAP 0.00638 0.43513 7.16511
22 1NU4 MLA 0.01664 0.40291 7.2165
23 1NOW IFG 0.005013 0.41172 8
24 1SS4 GSH 0.02422 0.41134 13.0719
25 2YD6 FLC 0.01337 0.4374 13.2075
26 3VHZ L2P GLC MAN SGA 0.03467 0.43288 14.5038
27 1T0S BML 0.00686 0.40585 19.7674
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