Receptor
PDB id Resolution Class Description Source Keywords
3E12 1.7 Å EC: 2.5.1.55 CU2+ SUBSTITUTED AQUIFEX AEOLICUS KDO8PS IN COMPLEX WITH KDO8P AQUIFEX AEOLICUS KDO KDO8PS COPPER PEP METAL GEOMETRY CYTOPLASM LIPOPOLYSACCHARIDE BIOSYNTHESIS TRANSFERASE
Ref.: ELECTRONIC STRUCTURE OF THE METAL CENTER IN THE CD(2+), ZN(2+), AND CU(2+) SUBSTITUTED FORMS OF KDO8P SYNTHASE: IMPLICATIONS FOR CATALYSIS. BIOCHEMISTRY V. 48 3610 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT B:501;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
CU A:270;
B:270;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
63.546 Cu [Cu+2...
KD0 A:268;
B:268;
 Valid;
Valid;
 none;
none;
 submit data
318.172 C8 H15 O11 P C([C@...
PO4 A:269;
B:269;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
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: KD0; Similar ligands found: 43
No: Ligand ECFP6 Tc MDL keys Tc
1 KD0 1 1
2 M2P 0.638889 0.914286
3 GOS 0.638889 0.914286
4 LG6 0.568182 1
5 6PG 0.568182 1
6 S6P 0.560976 0.861111
7 R10 0.55814 1
8 PA5 0.55814 1
9 I22 0.510638 0.916667
10 52L 0.510204 0.755556
11 TG6 0.5 0.916667
12 F6R 0.5 0.916667
13 1NT 0.490566 1
14 H4P 0.48 0.727273
15 P6T 0.479167 0.942857
16 2FP 0.479167 0.942857
17 PAN 0.479167 0.702128
18 P6F 0.479167 0.942857
19 M6R 0.478261 0.704545
20 AGP 0.478261 0.704545
21 G6Q 0.478261 0.970588
22 9C2 0.469388 0.6875
23 LX1 0.465116 0.861111
24 LXP 0.465116 0.837838
25 DX5 0.465116 0.837838
26 A5P 0.465116 0.837838
27 DEZ 0.454545 1
28 DER 0.454545 1
29 LRY 0.45283 0.75
30 R5P 0.434783 0.970588
31 DG6 0.434783 0.815789
32 R52 0.434783 0.970588
33 4TP 0.434783 0.829268
34 TX4 0.434783 0.659574
35 5SP 0.425532 0.891892
36 HMS 0.425532 0.891892
37 5RP 0.425532 0.891892
38 HG3 0.425 0.882353
39 O1B 0.418182 0.647059
40 PAI 0.418182 0.75
41 DXP 0.413043 0.861111
42 KDG 0.404762 0.638889
43 FQ8 0.4 0.864865
Similar Ligands (3D)
Ligand no: 1; Ligand: KD0; Similar ligands found: 1
No: Ligand Similarity coefficient
1 RUB 0.8515
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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