Receptor
PDB id Resolution Class Description Source Keywords
4PB4 1.8 Å EC: 4.3.1.27 D-THREO-3-HYDROXYASPARTATE DEHYDRATASE H351A MUTANT COMPLEXE AMINO MALEIC ACID DELFTIA SP. PLP ENZYME DEHYDRATASE METALLOPROTEIN 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
PLP 2KZ A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
358.199 n/a [P+](...
MG B:402;
A:402;
Invalid;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
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 2KZ; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 2KZ 1 1
2 PLP ALO 0.60274 0.9
3 CAN PLP 0.54321 0.818182
4 HEY 0.5375 0.875
5 GLY PLP 0.534247 0.847458
6 3LM 0.530864 0.848485
7 GAB PLP 0.52381 0.885246
8 GBC PLP 0.52381 0.885246
9 PLP SER 0.52 0.847458
10 P1T 0.513158 0.888889
11 PLP BH2 0.512821 0.864407
12 ASP PLP 0.506329 0.847458
13 PLP 0A0 0.506329 0.793651
14 SER PLP 0.5 0.881356
15 PLP 2TL 0.5 0.864407
16 PLP CYS 0.493671 0.881356
17 TZA PLP 0.488889 0.857143
18 PLP 2ML 0.487805 0.793651
19 SEP PLP 0.4875 0.847458
20 PLP SEP 0.4875 0.847458
21 LEU PLP 0.481481 0.819672
22 GLU PLP 0.47561 0.819672
23 PLP PMP 0.473684 0.777778
24 PLG 0.473684 0.84127
25 2BO 0.4625 0.854839
26 2BK 0.4625 0.854839
27 TLP 0.4625 0.854839
28 PLP MET 0.458824 0.757576
29 MET PLP 0.458824 0.757576
30 PPD 0.45679 0.84127
31 PDA 0.455696 0.854839
32 PP3 0.455696 0.854839
33 PDD 0.455696 0.854839
34 IK2 0.45 0.80303
35 5PA 0.444444 0.80303
36 PLS 0.444444 0.84127
37 PLP TYR 0.443182 0.85
38 C6P 0.439024 0.84127
39 IN5 0.435897 0.822581
40 PMG 0.435294 0.768116
41 PY5 0.433735 0.791045
42 PLA 0.433735 0.791045
43 RW2 0.426966 0.861538
44 PDG 0.423529 0.815385
45 PGU 0.423529 0.815385
46 7XF 0.423529 0.815385
47 CBA 0.423529 0.815385
48 ILP 0.423529 0.828125
49 QLP 0.418605 0.768116
50 PL2 0.418605 0.714286
51 PLP SUO 0.416667 0.776119
52 33P 0.414634 0.809524
53 76U 0.413793 0.80303
54 PY6 0.413793 0.768116
55 PMP HSA 0.413043 0.746269
56 PL4 0.411111 0.80303
57 PMH 0.409639 0.657895
58 N5F 0.409091 0.80303
59 EA5 0.409091 0.779412
60 PSZ 0.409091 0.779412
61 ORX 0.409091 0.80303
62 PE1 0.404494 0.80303
63 PXP 0.402778 0.766667
64 KAM 0.402174 0.80303
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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