Receptor
PDB id Resolution Class Description Source Keywords
3WQE 1.6 Å EC: 4.3.1.27 D-THREO-3-HYDROXYASPARTATE DEHYDRATASE FROM DELFTIA SP. HT23 WITH D-ALLOTHREONINE DELFTIA DEHYDRATASE PLP LYASE
Ref.: STRUCTURAL INSIGHTS INTO THE SUBSTRATE STEREOSPECIF D-THREO-3-HYDROXYASPARTATE DEHYDRATASE FROM DELFTIA HT23: A USEFUL ENZYME FOR THE SYNTHESIS OF OPTICALL L-THREO- AND D-ERYTHRO-3-HYDROXYASPARTATE APPL.MICROBIOL.BIOTECHNOL. V. 99 7137 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:402;
A:402;
B:404;
Part of Protein;
Part of Protein;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PLP 2TL A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
348.248 n/a [P+](...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WQD 1.5 Å EC: 4.3.1.27 D-THREO-3-HYDROXYASPARTATE DEHYDRATASE FROM DELFTIA SP. HT23 WITH D-ERYTHRO-3-HYDROXYASPARTATE DELFTIA DEHYDRATASE PLP LYASE
Ref.: STRUCTURAL INSIGHTS INTO THE SUBSTRATE STEREOSPECIF D-THREO-3-HYDROXYASPARTATE DEHYDRATASE FROM DELFTIA HT23: A USEFUL ENZYME FOR THE SYNTHESIS OF OPTICALL L-THREO- AND D-ERYTHRO-3-HYDROXYASPARTATE APPL.MICROBIOL.BIOTECHNOL. V. 99 7137 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3WQD Ki = 0.114 mM PLP 999 n/a n/a
2 3WQE - PLP 2TL n/a n/a
3 4PB5 - PLP BH2 n/a n/a
4 4PB4 - PLP 2KZ n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3WQD Ki = 0.114 mM PLP 999 n/a n/a
2 3WQE - PLP 2TL n/a n/a
3 4PB5 - PLP BH2 n/a n/a
4 4PB4 - PLP 2KZ 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 1 families.
1 3WQD Ki = 0.114 mM PLP 999 n/a n/a
2 3WQE - PLP 2TL n/a n/a
3 4PB5 - PLP BH2 n/a n/a
4 4PB4 - PLP 2KZ n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP 2TL; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 2TL 1 1
2 PLP BH2 0.8 0.962963
3 PLP SER 0.765625 0.944444
4 GLU PLP 0.714286 0.877193
5 SER PLP 0.705882 0.945455
6 LEU PLP 0.7 0.910714
7 PLP CYS 0.695652 0.910714
8 PLP SEP 0.685714 0.944444
9 SEP PLP 0.685714 0.944444
10 ASP PLP 0.685714 0.909091
11 MET PLP 0.64 0.836066
12 PLP MET 0.64 0.836066
13 GLY PLP 0.632353 0.909091
14 PLP TYR 0.615385 0.910714
15 PLP ALO 0.611111 0.929825
16 PLP 2ML 0.592105 0.87931
17 PLP 0A0 0.573333 0.87931
18 PLP HSA 0.52381 0.790323
19 PLP SUO 0.5 0.796875
20 PLP 2KZ 0.5 0.864407
21 CAN PLP 0.493976 0.784615
22 PLP PMP 0.48 0.862069
23 GBC PLP 0.45977 0.85
24 GAB PLP 0.45977 0.85
25 TZA PLP 0.445652 0.822581
26 TLP 0.432099 0.881356
27 2BO 0.432099 0.881356
28 2BK 0.432099 0.881356
29 PMP HSA 0.417582 0.765625
30 PPD 0.409639 0.806452
31 PXP 0.408451 0.789474
32 PDD 0.407407 0.85
33 PP3 0.407407 0.85
34 PDA 0.407407 0.85
35 PMP 0.402778 0.79661
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WQD; Ligand: PLP 999; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 3wqd.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JCM 137 0.002276 0.42295 1.5444
2 2NVA PL2 0.007921 0.41123 1.6129
3 5FAG PPI 0.00005609 0.49305 1.79487
4 1TUF AZ1 0.004268 0.42188 2.05128
5 2YG3 FAD 0.0104 0.42218 2.5641
6 4UTW RFW 0.006073 0.40007 2.5641
7 3TAO PGH 0.001317 0.41254 2.62172
8 2PLK P3D 0.005591 0.41159 2.82051
9 4HKP TKW 0.007468 0.4077 2.88462
10 4HKP 16B 0.008076 0.40086 2.88462
11 2QCD U5P 0.006213 0.40776 3.46154
12 1TRD PGH 0.003866 0.40011 4
13 5GJO PLP 0.001053 0.42701 4.10256
14 1M5W DXP 0.002778 0.44291 4.11523
15 1OC2 TDX 0.03678 0.40628 4.35897
16 1OC2 NAD 0.03678 0.40628 4.35897
17 2RJH DCS 0.00006739 0.47843 4.48549
18 5A5W GUO 0.007241 0.42873 4.74308
19 1EQ2 NAP 0.01521 0.4036 4.83871
20 4LUT DCS 0.00002438 0.50882 4.93506
21 1NJJ ORX 0.004804 0.41452 5.12821
22 3AYI HCI 0.02925 0.40993 5.12821
23 3AYI FAD 0.02833 0.40993 5.12821
24 1LBF 137 0.006758 0.41583 5.26316
25 1DQX BMP 0.006726 0.40802 5.38462
26 2OO0 PLP 0.004075 0.40739 5.89744
27 2SFP PPI 0.00003259 0.49688 5.92783
28 2YPI PGA 0.00207 0.40662 6.07287
29 1SW0 PGA 0.002272 0.40941 7.66129
30 3EXS 5RP 0.002928 0.40096 7.69231
31 2FLI DX5 0.006957 0.40558 7.72727
32 2VD9 EPC 0.00003131 0.50409 7.94872
33 2VD9 IN5 0.00003624 0.49514 7.94872
34 1ADO 13P 0.01039 0.40588 8.26446
35 2GAG FAD 0.0317 0.40305 10.101
36 1VFS DCS 0.00001615 0.51931 10.1036
37 4V15 PLP 0.000004079 0.51526 43.7995
Pocket No.: 2; Query (leader) PDB : 3WQD; Ligand: PLP 999; Similar sites found: 9
This union binding pocket(no: 2) in the query (biounit: 3wqd.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2IHK CSF 0.0201 0.40142 1.79487
2 5K8V 6RE 0.04745 0.40005 1.93906
3 4EYG VNL 0.003085 0.40134 2.71739
4 4ZCC FAD 0.04042 0.40153 5.05952
5 4ZCC NAI 0.04042 0.40153 5.05952
6 3QVP FAD 0.02803 0.40404 5.12821
7 2GAG FOA 0.03428 0.40137 10.101
8 3AD8 PYC 0.04438 0.40754 16.1616
9 3AD8 FAD 0.04438 0.40754 16.1616
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