Receptor
PDB id Resolution Class Description Source Keywords
5LNW 1.9 Å EC: 4.3.3.6 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PDX1-I320-G3P COMP ARABIDOPSIS THALIANA BETA/ALPHA BARREL PYRIDOXAL PHOSPHATE SYNTHASE GLUTAMINE AMIDOTRANSFERASE VITAMIN B6 BIOSYTHESIS LYASE
Ref.: LYSINE RELAY MECHANISM COORDINATES INTERMEDIATE TRA VITAMIN B6 BIOSYNTHESIS. NAT. CHEM. BIOL. V. 13 290 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K8P C:401;
D:401;
B:401;
A:401;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
269.189 C8 H16 N O7 P C[C@@...
HG3 C:403;
A:403;
D:403;
B:403;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
188.073 C3 H9 O7 P C([C@...
GOL A:404;
B:404;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
RP5 A:402;
C:402;
D:402;
B:402;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
230.11 C5 H11 O8 P C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LNW 1.9 Å EC: 4.3.3.6 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PDX1-I320-G3P COMP ARABIDOPSIS THALIANA BETA/ALPHA BARREL PYRIDOXAL PHOSPHATE SYNTHASE GLUTAMINE AMIDOTRANSFERASE VITAMIN B6 BIOSYTHESIS LYASE
Ref.: LYSINE RELAY MECHANISM COORDINATES INTERMEDIATE TRA VITAMIN B6 BIOSYNTHESIS. NAT. CHEM. BIOL. V. 13 290 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5LNW - HG3 C3 H9 O7 P C([C@H](C(....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5LNW - HG3 C3 H9 O7 P C([C@H](C(....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5LNW - HG3 C3 H9 O7 P C([C@H](C(....
2 3O05 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 3O07 - 1GP C3 H9 O6 P C([C@@H](C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HG3; Similar ligands found: 46
No: Ligand ECFP6 Tc MDL keys Tc
1 HG3 1 1
2 M2P 0.62963 0.852941
3 E4P 0.566667 0.90625
4 LXP 0.548387 0.828571
5 A5P 0.548387 0.828571
6 LX1 0.548387 0.852941
7 DX5 0.548387 0.828571
8 TX4 0.545455 0.644444
9 DER 0.53125 0.882353
10 S6P 0.53125 0.852941
11 DEZ 0.53125 0.882353
12 DXP 0.515152 0.852941
13 DG6 0.5 0.805556
14 R52 0.5 0.852941
15 R5P 0.5 0.852941
16 4TP 0.5 0.731707
17 R10 0.485714 0.882353
18 5SP 0.485714 0.783784
19 PA5 0.485714 0.882353
20 5RP 0.485714 0.783784
21 HMS 0.485714 0.783784
22 1GP 0.482759 0.90625
23 G3P 0.482759 0.90625
24 G6Q 0.472222 0.852941
25 M6R 0.472222 0.690476
26 RES 0.472222 0.617021
27 XBP 0.472222 0.828571
28 AGP 0.472222 0.690476
29 RUB 0.472222 0.828571
30 TG6 0.459459 0.805556
31 F6R 0.459459 0.805556
32 LG6 0.459459 0.882353
33 6PG 0.459459 0.882353
34 XDP 0.459459 0.857143
35 G3H 0.451613 0.875
36 3PG 0.451613 0.9375
37 P6T 0.435897 0.828571
38 P6F 0.435897 0.828571
39 PAN 0.435897 0.617021
40 I22 0.435897 0.805556
41 2FP 0.435897 0.828571
42 KD0 0.425 0.882353
43 CAP 0.404762 0.810811
44 H4P 0.404762 0.674419
45 52L 0.404762 0.666667
46 K8P 0.4 0.644444
Ligand no: 2; Ligand: RP5; Similar ligands found: 41
No: Ligand ECFP6 Tc MDL keys Tc
1 RP5 1 1
2 HSX 1 1
3 ABF 1 1
4 BGP 0.8 0.902439
5 M6D 0.8 0.902439
6 BG6 0.8 0.902439
7 A6P 0.8 0.902439
8 G6P 0.8 0.902439
9 M6P 0.8 0.902439
10 AHG 0.676471 0.880952
11 4R1 0.634146 0.755102
12 GLP 0.634146 0.755102
13 50A 0.615385 0.883721
14 RF5 0.615385 0.883721
15 GRF 0.589744 0.76
16 NNG 0.565217 0.685185
17 4QY 0.553191 0.685185
18 16G 0.553191 0.685185
19 BMX 0.553191 0.685185
20 FDQ 0.547619 0.860465
21 D6G 0.5 0.860465
22 G16 0.5 0.860465
23 PRP 0.5 0.975
24 1FT 0.490909 0.770833
25 N 0.47619 0.860465
26 PPC 0.469388 0.906977
27 T6P 0.469388 0.822222
28 32O 0.441176 0.675
29 RIB 0.441176 0.675
30 Z6J 0.441176 0.675
31 FUB 0.441176 0.675
32 AHR 0.441176 0.675
33 P3M 0.440678 0.822222
34 IRN 0.425926 0.606557
35 FGR 0.410714 0.655172
36 AHR AHR 0.404255 0.690476
37 TA6 0.404255 0.906977
38 F6P 0.404255 0.906977
39 FUB AHR 0.404255 0.690476
40 BNX 0.4 0.880952
41 ALX 0.4 0.880952
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5lnw.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5lnw.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5lnw.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5lnw.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5lnw.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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