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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:401;
B:406;
B:403;
A:402;
B:404;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PLP 999 A:401;
B:402;
Valid;
Valid;
none;
none;
Ki = 0.114 mM
374.198 n/a P(=O)...
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 999; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 999 1 1
2 MET PLP 0.641026 0.813559
3 PLP PHE 0.621951 0.888889
4 FEJ 0.56962 0.842105
5 PLP PVH 0.539326 0.765625
6 PLP MYB 0.534091 0.716418
7 F0G 0.532468 0.854545
8 KOU 0.525641 0.859649
9 PLP PUT 0.525 0.754098
10 EPC 0.52 0.818182
11 P70 0.5 0.824561
12 PL6 0.5 0.810345
13 0JO 0.5 0.79661
14 PLP 142 0.484211 0.793651
15 PL5 0.482759 0.770492
16 6DF 0.481928 0.77193
17 4LM 0.481013 0.810345
18 FEV 0.469136 0.79661
19 5DK 0.466667 0.75
20 EQJ 0.466667 0.75
21 PUS 0.465909 0.757576
22 EVM 0.463415 0.877193
23 PLP BH2 0.447059 0.816667
24 ASP PLP 0.447059 0.807018
25 Z98 0.44186 0.774194
26 EXT 0.4375 0.793103
27 HCP 0.428571 0.737705
28 PZP 0.424658 0.767857
29 PLP CYS 0.423529 0.746032
30 MPM 0.421687 0.775862
31 PLP 2TL 0.418605 0.786885
32 PLT 0.418367 0.758065
33 LLP 0.417582 0.761905
34 P3D 0.411765 0.703125
35 PLP 0.410959 0.796296
36 P89 0.408602 0.712121
37 AN7 0.407407 0.8
38 PLP 2KZ 0.406977 0.770492
39 FOO 0.402439 0.807018
40 GLU PLP 0.4 0.734375
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WQD; Ligand: PLP 999; Similar sites found with APoc: 90
This union binding pocket(no: 1) in the query (biounit: 3wqd.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 5YRJ BGC GLC 1.40845
2 5YRL GLC GLC 1.40845
3 5YRG BGC GLC 1.40845
4 6B2W AG2 1.5015
5 1JCM 137 1.5444
6 2NVA PL2 1.6129
7 1USI PHE 1.7341
8 4K91 SIN 1.7341
9 5FAG PPI 1.79487
10 1FDJ 13P 1.92837
11 1TUF AZ1 2.05128
12 4DE3 DN8 2.28137
13 2VPN 4CS 2.30769
14 1TKU 5RP 2.45098
15 2YG3 FAD 2.5641
16 4UTU LRY 2.5641
17 4UTW RFW 2.5641
18 3ZDS M8O 2.5641
19 3TAO PGH 2.62172
20 4F06 PHB 2.69542
21 4EYG VNL 2.71739
22 1EWK GLU 2.82051
23 2PLK P3D 2.82051
24 5L2M 6ZY 2.82051
25 5A1S FLC 2.82051
26 4HKP TKW 2.88462
27 4HKP 16B 2.88462
28 3OVR 5SP 3.07018
29 5A0U CHT 3.07692
30 5AHN IMP 3.33333
31 4IF4 BEF 3.36538
32 2QCD U5P 3.46154
33 5CSS G3P 3.53982
34 5ZI9 FLC 3.84615
35 4BI7 PGA 3.89105
36 1TRD PGH 4
37 5EYW PGA 4.01606
38 5GJO PLP 4.10256
39 5OC1 FAD 4.10256
40 1M5W DXP 4.11523
41 1GVF PGH 4.1958
42 5X2N ALA 4.35897
43 1OC2 NAD 4.35897
44 1OC2 TDX 4.35897
45 1LYX PGA 4.43548
46 2RJH DCS 4.48549
47 6BVE PGA 4.4898
48 4JEJ 1GP 4.5082
49 1L5Y BEF 4.51613
50 4B9E FAH 4.65116
51 5A5W GUO 4.74308
52 1EQ2 NAP 4.83871
53 3VPQ GSH 4.90196
54 4LUT DCS 4.93506
55 1NJJ ORX 5.12821
56 3AYI FAD 5.12821
57 3AYI HCI 5.12821
58 2FJK 13P 5.2459
59 1LBF 137 5.26316
60 1W8S FBP 5.32319
61 5G48 1FL 5.34759
62 1DQX BMP 5.38462
63 1QDS PGA 5.57769
64 1VKF CIT 5.85106
65 2OO0 PLP 5.89744
66 1NIU DCS 5.92783
67 2YPI PGA 6.07287
68 1MJT ITU 6.15385
69 5IXB LGA 6.48148
70 2ZE3 AKG 6.54545
71 5YJS SAL 6.92308
72 2BTM PGA 7.14286
73 1SW0 PGA 7.66129
74 3EXS 5RP 7.69231
75 2FLI DX5 7.72727
76 2VD9 EPC 7.94872
77 2VD9 IN5 7.94872
78 5FAW CHT 7.94872
79 1ADO 13P 8.26446
80 4YMZ 13P 8.36653
81 4NAE 1GP 8.44444
82 1MFI FHC 8.77193
83 2GAG FAD 10.101
84 1VFS DCS 10.1036
85 3FGZ BEF 10.1562
86 4LWM MHO 11.0599
87 3GCM 5GP 12.1951
88 3Q9T FAY 13.3333
89 2F6U CIT 17.9487
90 4V15 PLP 43.7995
Pocket No.: 2; Query (leader) PDB : 3WQD; Ligand: PLP 999; Similar sites found with APoc: 15
This union binding pocket(no: 2) in the query (biounit: 3wqd.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 2IHK CSF 1.79487
2 2AJH MET 3.33333
3 4LOC OXM 3.58974
4 1SBR VIB 4
5 2PYY GLU 4.38596
6 4XW2 SIM 4.54545
7 1ZED PNP 4.61538
8 4ZCC FAD 5.05952
9 4ZCC NAI 5.05952
10 3QVP FAD 5.12821
11 4MBY BGC SIA GAL 6.11511
12 3AIH BMA MAN MAN 9.67742
13 2GAG FOA 10.101
14 3AD8 PYC 16.1616
15 3AD8 FAD 16.1616
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