Receptor
PDB id Resolution Class Description Source Keywords
1JCX 1.8 Å EC: 2.5.1.55 AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH API AND CADM AQUIFEX AEOLICUS KDO8PS KDO8P KDO API BETA/ALPHA BARREL LYASE
Ref.: STRUCTURES OF AQUIFEX AEOLICUS KDO8P SYNTHASE IN CO WITH R5P AND PEP, AND WITH A BISUBSTRATE INHIBITOR: ACTIVE SITE WATER IN CATALYSIS. BIOCHEMISTRY V. 40 15676 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CD A:1270;
B:2270;
 Invalid;
Invalid;
 none;
none;
 submit data
112.411 Cd [Cd+2...
PAI A:1300;
B:2300;
 Valid;
Valid;
 none;
none;
 Ki = 7 uM
415.225 C9 H23 N O13 P2 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2NX1 1.8 Å EC: 2.5.1.55 STRUCTURAL AND MECHANISTIC CHANGES ALONG AN ENGINEERED PATH METALLO TO NON-METALLO KDO8P SYNTHASE AQUIFEX AEOLICUS KDO KDO8P KDO8PS PEP A5P RP5 TRANSFERASE
Ref.: STRUCTURAL AND MECHANISTIC CHANGES ALONG AN ENGINEE FROM METALLO TO NONMETALLO 3-DEOXY-D-MANNO-OCTULOSO 8-PHOSPHATE SYNTHASES. BIOCHEMISTRY V. 46 4532 2007
Members (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2A2I Kd = 0.04 uM A5P C5 H13 O8 P C([C@H]([C....
2 1LRQ - PEP C3 H5 O6 P C=C(C(=O)O....
3 1ZJI - R5P C5 H11 O8 P C(C(C(C(C=....
4 1FY6 - A5P C5 H13 O8 P C([C@H]([C....
5 3E12 - KD0 C8 H15 O11 P C([C@H]([C....
6 1ZHA Kd = 0.04 uM PEP C3 H5 O6 P C=C(C(=O)O....
7 2NWS Kd = 5.44 uM A5P C5 H13 O8 P C([C@H]([C....
8 1T8X - PEP C3 H5 O6 P C=C(C(=O)O....
9 2NWR - PEP C3 H5 O6 P C=C(C(=O)O....
10 1FXQ - PEP C3 H5 O6 P C=C(C(=O)O....
11 1FWN - PEP C3 H5 O6 P C=C(C(=O)O....
12 1JCY - PEP C3 H5 O6 P C=C(C(=O)O....
13 1LRO - PEP C3 H5 O6 P C=C(C(=O)O....
14 1PCK - PEZ C4 H9 O6 P CCC(C(=O)O....
15 3E0I - PEP C3 H5 O6 P C=C(C(=O)O....
16 2NXG Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
17 2NXI - PEP C3 H5 O6 P C=C(C(=O)O....
18 2NX3 Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
19 1T96 - PEP C3 H5 O6 P C=C(C(=O)O....
20 2NXH - PEP C3 H5 O6 P C=C(C(=O)O....
21 2EF9 Kd = 14.18 uM A5P C5 H13 O8 P C([C@H]([C....
22 1FWT - E4P C4 H9 O7 P C([C@H]([C....
23 1PE1 - 2PG C3 H7 O7 P C([C@H](C(....
24 2A21 - PEP C3 H5 O6 P C=C(C(=O)O....
25 2NX1 Kd = 0.02 uM RP5 C5 H11 O8 P C([C@@H]1[....
26 1JCX Ki = 7 uM PAI C9 H23 N O13 P2 C([C@H]([C....
27 1FWW - PEP C3 H5 O6 P C=C(C(=O)O....
28 1FWS - PEP C3 H5 O6 P C=C(C(=O)O....
29 1PCW - H4P C7 H19 N O11 P2 C([C@H]([C....
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2A2I Kd = 0.04 uM A5P C5 H13 O8 P C([C@H]([C....
2 1LRQ - PEP C3 H5 O6 P C=C(C(=O)O....
3 1ZJI - R5P C5 H11 O8 P C(C(C(C(C=....
4 1FY6 - A5P C5 H13 O8 P C([C@H]([C....
5 3E12 - KD0 C8 H15 O11 P C([C@H]([C....
6 1ZHA Kd = 0.04 uM PEP C3 H5 O6 P C=C(C(=O)O....
7 2NWS Kd = 5.44 uM A5P C5 H13 O8 P C([C@H]([C....
8 1T8X - PEP C3 H5 O6 P C=C(C(=O)O....
9 2NWR - PEP C3 H5 O6 P C=C(C(=O)O....
10 1FXQ - PEP C3 H5 O6 P C=C(C(=O)O....
11 1FWN - PEP C3 H5 O6 P C=C(C(=O)O....
12 1JCY - PEP C3 H5 O6 P C=C(C(=O)O....
13 1LRO - PEP C3 H5 O6 P C=C(C(=O)O....
14 1PCK - PEZ C4 H9 O6 P CCC(C(=O)O....
15 3E0I - PEP C3 H5 O6 P C=C(C(=O)O....
16 2NXG Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
17 2NXI - PEP C3 H5 O6 P C=C(C(=O)O....
18 2NX3 Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
19 1T96 - PEP C3 H5 O6 P C=C(C(=O)O....
20 2NXH - PEP C3 H5 O6 P C=C(C(=O)O....
21 2EF9 Kd = 14.18 uM A5P C5 H13 O8 P C([C@H]([C....
22 1FWT - E4P C4 H9 O7 P C([C@H]([C....
23 1PE1 - 2PG C3 H7 O7 P C([C@H](C(....
24 2A21 - PEP C3 H5 O6 P C=C(C(=O)O....
25 2NX1 Kd = 0.02 uM RP5 C5 H11 O8 P C([C@@H]1[....
26 1JCX Ki = 7 uM PAI C9 H23 N O13 P2 C([C@H]([C....
27 1FWW - PEP C3 H5 O6 P C=C(C(=O)O....
28 1FWS - PEP C3 H5 O6 P C=C(C(=O)O....
29 1PCW - H4P C7 H19 N O11 P2 C([C@H]([C....
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1PHW Ki = 0.5 mM N C5 H11 O7 P C1[C@@H]([....
2 1G7V Kd = 0.4 uM PAI C9 H23 N O13 P2 C([C@H]([C....
3 4Z1D - PEP C3 H5 O6 P C=C(C(=O)O....
4 2A2I Kd = 0.04 uM A5P C5 H13 O8 P C([C@H]([C....
5 1LRQ - PEP C3 H5 O6 P C=C(C(=O)O....
6 1ZJI - R5P C5 H11 O8 P C(C(C(C(C=....
7 1FY6 - A5P C5 H13 O8 P C([C@H]([C....
8 3E12 - KD0 C8 H15 O11 P C([C@H]([C....
9 1ZHA Kd = 0.04 uM PEP C3 H5 O6 P C=C(C(=O)O....
10 2NWS Kd = 5.44 uM A5P C5 H13 O8 P C([C@H]([C....
11 1T8X - PEP C3 H5 O6 P C=C(C(=O)O....
12 2NWR - PEP C3 H5 O6 P C=C(C(=O)O....
13 1FXQ - PEP C3 H5 O6 P C=C(C(=O)O....
14 1FWN - PEP C3 H5 O6 P C=C(C(=O)O....
15 1JCY - PEP C3 H5 O6 P C=C(C(=O)O....
16 1LRO - PEP C3 H5 O6 P C=C(C(=O)O....
17 1PCK - PEZ C4 H9 O6 P CCC(C(=O)O....
18 3E0I - PEP C3 H5 O6 P C=C(C(=O)O....
19 2NXG Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
20 2NXI - PEP C3 H5 O6 P C=C(C(=O)O....
21 2NX3 Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
22 1T96 - PEP C3 H5 O6 P C=C(C(=O)O....
23 2NXH - PEP C3 H5 O6 P C=C(C(=O)O....
24 2EF9 Kd = 14.18 uM A5P C5 H13 O8 P C([C@H]([C....
25 1FWT - E4P C4 H9 O7 P C([C@H]([C....
26 1PE1 - 2PG C3 H7 O7 P C([C@H](C(....
27 2A21 - PEP C3 H5 O6 P C=C(C(=O)O....
28 2NX1 Kd = 0.02 uM RP5 C5 H11 O8 P C([C@@H]1[....
29 1JCX Ki = 7 uM PAI C9 H23 N O13 P2 C([C@H]([C....
30 1FWW - PEP C3 H5 O6 P C=C(C(=O)O....
31 1FWS - PEP C3 H5 O6 P C=C(C(=O)O....
32 1PCW - H4P C7 H19 N O11 P2 C([C@H]([C....
33 3FYP - PEP C3 H5 O6 P C=C(C(=O)O....
34 3FYO - PEP C3 H5 O6 P C=C(C(=O)O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PAI; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 PAI 1 1
2 M2P 0.547619 0.767442
3 GOS 0.547619 0.767442
4 S6P 0.489362 0.727273
5 AGP 0.45098 0.75
6 M6R 0.45098 0.75
7 G6Q 0.45098 0.727273
8 H4P 0.428571 0.888889
9 KD0 0.418182 0.75
10 LG6 0.415094 0.75
11 6PG 0.415094 0.75
12 R5P 0.411765 0.727273
13 TX4 0.411765 0.673077
14 R52 0.411765 0.727273
15 LXP 0.408163 0.711111
16 A5P 0.408163 0.711111
17 DX5 0.408163 0.711111
18 LX1 0.408163 0.688889
19 I22 0.4 0.733333
Similar Ligands (3D)
Ligand no: 1; Ligand: PAI; Similar ligands found: 1
No: Ligand Similarity coefficient
1 1NT 0.8771
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NX1; Ligand: PEP; Similar sites found with APoc: 9
This union binding pocket(no: 1) in the query (biounit: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1RZM PEP 45.3184
2 3TFC PEP 46.4419
3 3TFC PEP 46.4419
4 4C1K PEP 48.0916
5 4C1K PEP 48.0916
6 4C1K PEP 48.0916
7 4C1K PEP 48.0916
8 4C1K PEP 48.0916
9 4C1K PEP 48.0916
Pocket No.: 2; Query (leader) PDB : 2NX1; Ligand: PEP; 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: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2NX1; Ligand: RP5; Similar sites found with APoc: 9
This union binding pocket(no: 3) in the query (biounit: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1RZM PEP 45.3184
2 3TFC PEP 46.4419
3 3TFC PEP 46.4419
4 4C1K PEP 48.0916
5 4C1K PEP 48.0916
6 4C1K PEP 48.0916
7 4C1K PEP 48.0916
8 4C1K PEP 48.0916
9 4C1K PEP 48.0916
Pocket No.: 4; Query (leader) PDB : 2NX1; 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: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2NX1; Ligand: PEP; Similar sites found with APoc: 9
This union binding pocket(no: 5) in the query (biounit: 2nx1.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1RZM PEP 45.3184
2 3TFC PEP 46.4419
3 3TFC PEP 46.4419
4 4C1K PEP 48.0916
5 4C1K PEP 48.0916
6 4C1K PEP 48.0916
7 4C1K PEP 48.0916
8 4C1K PEP 48.0916
9 4C1K PEP 48.0916
Pocket No.: 6; Query (leader) PDB : 2NX1; Ligand: PEP; 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: 2nx1.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2NX1; Ligand: RP5; Similar sites found with APoc: 9
This union binding pocket(no: 7) in the query (biounit: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1RZM PEP 45.3184
2 3TFC PEP 46.4419
3 3TFC PEP 46.4419
4 4C1K PEP 48.0916
5 4C1K PEP 48.0916
6 4C1K PEP 48.0916
7 4C1K PEP 48.0916
8 4C1K PEP 48.0916
9 4C1K PEP 48.0916
Pocket No.: 8; Query (leader) PDB : 2NX1; 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: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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