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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PEP A:1268;
B:2268;
Valid;
Valid;
none;
none;
submit data
168.042 C3 H5 O6 P C=C(C...
RP5 A:1269;
B:2269;
Valid;
Valid;
none;
none;
Kd = 0.02 uM
230.11 C5 H11 O8 P 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
Ligand no: 1; Ligand: PEP; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 PEP 1 1
2 UVW 0.44 0.709677
Ligand no: 2; Ligand: RP5; Similar ligands found: 43
No: Ligand ECFP6 Tc MDL keys Tc
1 ABF 1 1
2 HSX 1 1
3 RP5 1 1
4 A6P 0.8 0.902439
5 M6P 0.8 0.902439
6 G6P 0.8 0.902439
7 BGP 0.8 0.902439
8 M6D 0.8 0.902439
9 BG6 0.8 0.902439
10 AHG 0.676471 0.880952
11 GLP 0.634146 0.755102
12 4R1 0.634146 0.755102
13 RF5 0.615385 0.883721
14 50A 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 XYT 0.5 0.822222
23 PRP 0.5 0.975
24 G16 0.5 0.860465
25 D6G 0.5 0.860465
26 1FT 0.490909 0.770833
27 N 0.47619 0.860465
28 PPC 0.469388 0.906977
29 T6P 0.469388 0.822222
30 Z6J 0.441176 0.675
31 RIB 0.441176 0.675
32 FUB 0.441176 0.675
33 32O 0.441176 0.675
34 AHR 0.441176 0.675
35 P3M 0.440678 0.822222
36 IRN 0.425926 0.606557
37 FGR 0.410714 0.655172
38 FUB AHR 0.404255 0.690476
39 F6P 0.404255 0.906977
40 TA6 0.404255 0.906977
41 AHR AHR 0.404255 0.690476
42 ALX 0.4 0.880952
43 BNX 0.4 0.880952
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: 65
This union binding pocket(no: 1) in the query (biounit: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 4K55 H6P None
2 1B74 DGN 0.787402
3 3UYW TAU 0.934579
4 5GLT BGC GAL NAG GAL 1.1236
5 3UXL CFI 1.49813
6 5T9C G3P 1.87266
7 5FYR INS 1.87266
8 1M3U KPL 1.89394
9 1L5Y BEF 1.93548
10 1YHM AHD 2.24719
11 1MUU SUC 2.24719
12 1O5Q PYR 2.24719
13 2VAR KDF 2.62172
14 2VAR KDG 2.62172
15 2HIM ASN 2.62172
16 2HIM ASP 2.62172
17 5UC9 MYR 2.65487
18 3U6W KIV 2.99625
19 1XIM XYL 2.99625
20 4BJ8 BTN 3.1746
21 5UXM PEP 3.37079
22 1UZ4 IFL 3.37079
23 2DKD NG1 3.37079
24 6FU4 HSM 3.37079
25 4K10 NI9 3.37079
26 6C4A PYR 3.37079
27 1IGW PYR 3.37079
28 4D1J DGJ 3.74532
29 1HSL HIS 3.78151
30 2Y7G AAE 4.11985
31 2BMB PMM 4.49438
32 1IXE CIT 4.49438
33 5W3Y ACO 4.86891
34 1XF1 CIT 5.24345
35 3MI3 LYS 5.24345
36 1AJ8 CIT 5.99251
37 6GN6 GLC 6.04027
38 1SQL GUN 6.16438
39 1NX9 AIC 6.36704
40 3QTP 2PG 6.74157
41 2J73 GLC GLC GLC GLC 6.79612
42 2QRD ADP 7.2165
43 4AMW 5DI 7.49064
44 3PAK MAN 8.10811
45 5CKS 52L 8.61423
46 5OSW DIU 8.98876
47 1XS5 MET 9.12863
48 1OF8 G3P 9.73783
49 1OF8 PEP 9.73783
50 3DG6 MUC 9.73783
51 3KFF XBT 9.87654
52 3KFF ZBT 9.87654
53 4UMA GZ3 10.1124
54 5E9G GLV 10.8614
55 4JCA CIT 11.3772
56 4JLS 3ZE 11.8421
57 5ZCO PGV 13.7615
58 3H22 B53 14.2322
59 6G1O GLV 14.6067
60 4UOZ GLA 19.8502
61 1DCP HBI 23.0769
62 1RZM PEP 45.3184
63 1RZM E4P 45.3184
64 3TFC PEP 46.4419
65 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: 67
This union binding pocket(no: 3) in the query (biounit: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1B74 DGN 0.787402
2 3UYW TAU 0.934579
3 5GLT BGC GAL NAG GAL 1.1236
4 5T9C G3P 1.87266
5 3ORQ ADP 1.87266
6 5FYR INS 1.87266
7 1G0C CBI 1.87266
8 1L5Y BEF 1.93548
9 4D4U FUC GAL NAG 2.24719
10 1MUU SUC 2.24719
11 1O5Q PYR 2.24719
12 1YHM AHD 2.24719
13 2HIM ASN 2.62172
14 2HIM ASP 2.62172
15 2UWN SCR 2.6738
16 3U6W KIV 2.99625
17 1SR9 KIV 2.99625
18 3MA0 XYP 2.99625
19 1XIM XYL 2.99625
20 3WBZ ATP 2.99625
21 4BJ8 BTN 3.1746
22 5UXM PEP 3.37079
23 1UZ4 IFL 3.37079
24 6FU4 HSM 3.37079
25 4GN8 ASO 3.37079
26 1IGW PYR 3.37079
27 2DKD NG1 3.37079
28 6C4A PYR 3.37079
29 4K10 NI9 3.37079
30 1GYM MYG 3.74532
31 1EKX PAL 3.74532
32 1HSL HIS 3.78151
33 5KK4 44E 4.16667
34 1VKF CIT 4.25532
35 2BMB PMM 4.49438
36 1IXE CIT 4.49438
37 1XF1 CIT 5.24345
38 3MI3 LYS 5.24345
39 2VGK REZ 5.24345
40 5BRP PNG 5.24345
41 1AJ8 CIT 5.99251
42 4BXF AKG 5.99251
43 2DW7 SRT 5.99251
44 6GN6 GLC 6.04027
45 1SQL GUN 6.16438
46 1SO0 GAL 6.36704
47 3QTP 2PG 6.74157
48 4PU6 ASP 6.87023
49 2QRD ADP 7.2165
50 5CKS 52L 8.61423
51 1OF8 G3P 9.73783
52 1OF8 PEP 9.73783
53 4UMA GZ3 10.1124
54 2QX0 PH2 10.6918
55 2O1O RIS 10.8614
56 5E9G GLV 10.8614
57 4JCA CIT 11.3772
58 4JLS 3ZE 11.8421
59 5C8W PCG 11.8881
60 5ZCO PGV 13.7615
61 3H22 B53 14.2322
62 1DCP HBI 23.0769
63 4EXO PYR 23.2877
64 1RZM PEP 45.3184
65 1RZM E4P 45.3184
66 3TFC PEP 46.4419
67 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: 17
This union binding pocket(no: 5) in the query (biounit: 2nx1.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1G0C CBI 1.87266
2 4D4U FUC GAL NAG 2.24719
3 1SR9 KIV 2.99625
4 3LDW ZOL 3.74532
5 3T7V MD0 4.11985
6 5KK4 44E 4.16667
7 1VKF CIT 4.25532
8 3EJW PAV 5.99251
9 3W5N RAM 5.99251
10 1SO0 GAL 6.36704
11 2FVK DUC 6.36704
12 1DRJ RIP 7.11611
13 4AVV CD 7.84314
14 2QX0 PH2 10.6918
15 2O1O RIS 10.8614
16 5C8W PCG 11.8881
17 2IOY RIP 12.7341
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: 20
This union binding pocket(no: 7) in the query (biounit: 2nx1.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 4K55 H6P None
2 3UXL CFI 1.49813
3 1M3U KPL 1.89394
4 2VAR KDF 2.62172
5 2VAR KDG 2.62172
6 5UC9 MYR 2.65487
7 4D1J DGJ 3.74532
8 2Y7G AAE 4.11985
9 5W3Y ACO 4.86891
10 1NX9 AIC 6.36704
11 2J73 GLC GLC GLC GLC 6.79612
12 4AMW 5DI 7.49064
13 3PAK MAN 8.10811
14 5OSW DIU 8.98876
15 1XS5 MET 9.12863
16 3DG6 MUC 9.73783
17 3KFF XBT 9.87654
18 3KFF ZBT 9.87654
19 6G1O GLV 14.6067
20 4UOZ GLA 19.8502
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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