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 1 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: 49
No: Ligand ECFP6 Tc MDL keys Tc
1 HG3 1 1
2 M2P 0.62963 0.852941
3 GOS 0.62963 0.852941
4 E4P 0.566667 0.90625
5 DX5 0.548387 0.828571
6 LX1 0.548387 0.852941
7 A5P 0.548387 0.828571
8 LXP 0.548387 0.828571
9 TX4 0.545455 0.644444
10 S6P 0.53125 0.852941
11 DER 0.53125 0.882353
12 DEZ 0.53125 0.882353
13 DXP 0.515152 0.852941
14 4TP 0.5 0.731707
15 R52 0.5 0.852941
16 DG6 0.5 0.805556
17 R5P 0.5 0.852941
18 5RP 0.485714 0.783784
19 HMS 0.485714 0.783784
20 R10 0.485714 0.882353
21 5SP 0.485714 0.783784
22 PA5 0.485714 0.882353
23 1GP 0.482759 0.90625
24 G3P 0.482759 0.90625
25 XBP 0.472222 0.828571
26 RUB 0.472222 0.828571
27 AGP 0.472222 0.690476
28 M6R 0.472222 0.690476
29 G6Q 0.472222 0.852941
30 RES 0.472222 0.617021
31 LG6 0.459459 0.882353
32 6PG 0.459459 0.882353
33 TG6 0.459459 0.805556
34 XDP 0.459459 0.857143
35 F6R 0.459459 0.805556
36 3PG 0.451613 0.9375
37 G3H 0.451613 0.875
38 FQ8 0.447368 0.805556
39 PAN 0.435897 0.617021
40 P6T 0.435897 0.828571
41 I22 0.435897 0.805556
42 P6F 0.435897 0.828571
43 2FP 0.435897 0.828571
44 9C2 0.425 0.604167
45 KD0 0.425 0.882353
46 CAP 0.404762 0.810811
47 H4P 0.404762 0.674419
48 52L 0.404762 0.666667
49 K8P 0.4 0.644444
Ligand no: 2; Ligand: RP5; Similar ligands found: 45
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 BG6 0.8 0.902439
6 A6P 0.8 0.902439
7 M6P 0.8 0.902439
8 M6D 0.8 0.902439
9 G6P 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 16G 0.553191 0.685185
18 4QY 0.553191 0.685185
19 BMX 0.553191 0.685185
20 FDQ 0.547619 0.860465
21 RI2 0.534884 0.95
22 G16 0.5 0.860465
23 D6G 0.5 0.860465
24 XYT 0.5 0.822222
25 PRP 0.5 0.975
26 1FT 0.490909 0.770833
27 N 0.47619 0.860465
28 T6P 0.469388 0.822222
29 PPC 0.469388 0.906977
30 BDR 0.441176 0.675
31 RIB 0.441176 0.675
32 Z6J 0.441176 0.675
33 FUB 0.441176 0.675
34 32O 0.441176 0.675
35 AHR 0.441176 0.675
36 P3M 0.440678 0.822222
37 IRN 0.425926 0.606557
38 QIF 0.425532 0.860465
39 FGR 0.410714 0.655172
40 AHR AHR 0.404255 0.690476
41 TA6 0.404255 0.906977
42 FUB AHR 0.404255 0.690476
43 F6P 0.404255 0.906977
44 BNX 0.4 0.880952
45 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 with APoc: 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 Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: 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 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: 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 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: 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 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: 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 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5lnw.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 5lnw.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 5lnw.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 15; Query (leader) PDB : 5LNW; Ligand: RP5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 15) in the query (biounit: 5lnw.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 16; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 16) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 17; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 17) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 18; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 18) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 19; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 19) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 20; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 20) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 21; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 21) in the query (biounit: 5lnw.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 22; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 22) in the query (biounit: 5lnw.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 23; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 23) in the query (biounit: 5lnw.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 24; Query (leader) PDB : 5LNW; Ligand: HG3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 24) in the query (biounit: 5lnw.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
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