Receptor
PDB id Resolution Class Description Source Keywords
1GG1 2 Å EC: 4.1.2.15 CRYSTAL STRUCTURE ANALYSIS OF DAHP SYNTHASE IN COMPLEX WITH MN2+ AND 2-PHOSPHOGLYCOLATE ESCHERICHIA COLI BETA-ALPHA-BARREL LYASE
Ref.: STRUCTURE OF 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM ESCHERICHIA COLI: COMPARISON OF THE MN(2+)*2-PHOSPHOGLYCOLATE AND THE PB(2+)*2-PHOSPHOENOLPYRUVATE COMPLEXES AND IMPLICATIONS FOR CATALYSIS. J.MOL.BIOL. V. 301
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN A:371;
B:371;
C:371;
D:371;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
PGA A:372;
B:372;
C:372;
D:372;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
156.031 C2 H5 O6 P C(C(=...
SO4 A:1373;
A:1374;
B:2373;
B:2374;
C:3373;
C:3374;
D:4373;
D:4374;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CKS 2.12 Å EC: 4.1.2.15 DAHP (3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE) SYNTHASE I WITH DAHP OXIME. ESCHERICHIA COLI (STRAIN K12) DAHP SYNTHASE INHIBITOR COMPLEX TRANSITION STATE MIMIC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: POTENT INHIBITION OF 3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE (DAHP) S BY DAHP OXIME, A PHOSPHATE GROUP MIMIC. BIOCHEMISTRY V. 55 6617 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
2 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
3 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
9 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
10 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
11 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
9 1OAB - PEP C3 H5 O6 P C=C(C(=O)O....
10 1OFO - PGA C2 H5 O6 P C(C(=O)O)O....
11 1OF6 - DTY C9 H11 N O3 c1cc(ccc1C....
12 1OF8 - G3P C3 H9 O6 P C([C@H](CO....
13 1OFA - PEP C3 H5 O6 P C=C(C(=O)O....
14 1HFB - PEP C3 H5 O6 P C=C(C(=O)O....
15 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
16 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
17 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PGA; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 PGA 1 1
2 HPV 0.555556 0.903226
3 13P 0.5 0.818182
4 PGH 0.482759 0.651163
5 3PG 0.433333 0.90625
6 3PP 0.423077 0.866667
7 EFS 0.416667 0.741935
8 PAE 0.416667 0.806452
9 SEP 0.40625 0.710526
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CKS; Ligand: 52L; Similar sites found: 14
This union binding pocket(no: 1) in the query (biounit: 5cks.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Z8O DEB 0.006914 0.42688 2.5641
2 3WCA FPS 0.0172 0.40752 3.1339
3 3FYP PEP 0.00006515 0.47042 3.57143
4 5M7Y MAN MAN MAN 0.01129 0.40339 3.7037
5 2GQT FAD 0.04023 0.41139 4.47761
6 3FQ8 PMP 0.009052 0.41669 4.8433
7 2D7C GTP 0.01813 0.40359 6.58683
8 1H6H PIB 0.02378 0.40102 7.69231
9 2NX1 PEP 0.0008425 0.50448 8.61423
10 2NX1 RP5 0.0009781 0.50106 8.61423
11 4BV6 FAD 0.04686 0.40032 10.5413
12 4Z1D PEP 0.0000009851 0.51768 16.3043
13 1M3U KPL 0.01285 0.40268 17.803
14 4C1K PEP 0.00005406 0.52946 24.4275
Pocket No.: 2; Query (leader) PDB : 5CKS; Ligand: GAL; Similar sites found: 38
This union binding pocket(no: 2) in the query (biounit: 5cks.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4P6X HCY 0.009516 0.42219 1.96078
2 3KFC 61X 0.04776 0.40449 1.97628
3 1XPK HMG 0.04416 0.40238 1.9943
4 2Q97 ATP 0.03123 0.40096 2.849
5 3GN8 DEX 0.01287 0.41544 3.21285
6 1YYE 196 0.01554 0.40446 3.35821
7 1YNH SUO 0.01692 0.41124 3.4188
8 3QFS FAD 0.03416 0.41361 3.7037
9 3QFS NAP 0.03416 0.41361 3.7037
10 2ZID GLC GLC GLC 0.01703 0.40305 3.7037
11 4J26 EST 0.005371 0.42316 3.75
12 4J24 EST 0.008678 0.40882 3.75
13 3ICS COA 0.03365 0.413 3.9886
14 4DXJ IPE 0.01443 0.42951 4.2735
15 4DXJ 0M9 0.01962 0.42106 4.2735
16 5GVL GI8 0.03124 0.40881 4.2735
17 5GVL PLG 0.03124 0.40881 4.2735
18 2VW1 DAN 0.02587 0.40757 4.2735
19 2PT9 S4M 0.03586 0.40122 4.36137
20 4LSJ LSJ 0.0126 0.415 4.65116
21 4R38 RBF 0.02152 0.41255 5
22 3WQQ NDP 0.04121 0.41373 5.12821
23 3WQQ IB3 0.04121 0.41373 5.12821
24 3V49 PK0 0.009104 0.43192 5.26316
25 1LAF ARG 0.01514 0.41653 6.30252
26 4J0M BLD 0.02059 0.40321 6.55271
27 3KRO IPE 0.02783 0.40821 6.56934
28 3KRO DST 0.02783 0.40821 6.56934
29 1N62 MCN 0.008478 0.45026 6.62651
30 3FS1 MYR 0.005742 0.42558 6.95652
31 5KY3 GFB 0.02282 0.40513 7.5
32 5DT6 GLU 0.01561 0.40032 7.86517
33 5ETJ IM5 0.02442 0.40254 8.64198
34 2XCM ADP 0.00284 0.44439 8.69565
35 3OJI PYV 0.0172 0.41151 12.6984
36 2AIB ERG 0.0278 0.40303 13.2653
37 4M8E 29V 0.01096 0.4192 17.7489
38 3H0A 9RA 0.01076 0.41843 22.0588
39 1PZL MYR 0.005409 0.43026 50
Pocket No.: 3; Query (leader) PDB : 5CKS; Ligand: 52L; 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: 5cks.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5CKS; Ligand: GAL; 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: 5cks.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5CKS; Ligand: GAL; 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: 5cks.bio1) has 3 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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