Receptor
PDB id Resolution Class Description Source Keywords
5KZD 2.33 Å EC: 4.1.3.3 N-ACETYLNEURAMINATE LYASE FROM METHICILLIN-RESISTANT STAPHYL AUREUS WITH BOUND SIALIC ACID ALDITOL STAPHYLOCOCCUS AUREUS (STRAIN USA300) TIM-BARREL INHIBITOR N-ACETYLNEURAMINATE LYASE LYASE
Ref.: STRUCTURE AND INHIBITION OF N-ACETYLNEURAMINATE LYA METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS. FEBS LETT. V. 590 4414 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RCJ A:301;
B:301;
C:301;
D:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 0.39 mM
311.286 C11 H21 N O9 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KZD 2.33 Å EC: 4.1.3.3 N-ACETYLNEURAMINATE LYASE FROM METHICILLIN-RESISTANT STAPHYL AUREUS WITH BOUND SIALIC ACID ALDITOL STAPHYLOCOCCUS AUREUS (STRAIN USA300) TIM-BARREL INHIBITOR N-ACETYLNEURAMINATE LYASE LYASE
Ref.: STRUCTURE AND INHIBITION OF N-ACETYLNEURAMINATE LYA METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS. FEBS LETT. V. 590 4414 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5KZD Ki = 0.39 mM RCJ C11 H21 N O9 CC(=O)N[C@....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4IMF - SI3 C11 H19 N O9 CC(=O)N[C@....
2 4IMG - NGF C11 H19 N O10 C([C@@H]([....
3 1F73 Ki = 4.1 mM HMN C11 H21 N O9 CC(=O)N[C@....
4 1F74 Ki = 0.9 mM NAY C11 H19 N O8 CC(=O)N[C@....
5 5KZD Ki = 0.39 mM RCJ C11 H21 N O9 CC(=O)N[C@....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2WPB Ki = 1.3 mM ZZI C10 H21 N O4 CCCN(CCC)C....
2 2WNZ - LAC C3 H6 O3 C[C@H](C(=....
3 2XFW - PYR C3 H4 O3 CC(=O)C(=O....
4 2WKJ - PYR C3 H4 O3 CC(=O)C(=O....
5 4IMF - SI3 C11 H19 N O9 CC(=O)N[C@....
6 4IMG - NGF C11 H19 N O10 C([C@@H]([....
7 1F73 Ki = 4.1 mM HMN C11 H21 N O9 CC(=O)N[C@....
8 1F74 Ki = 0.9 mM NAY C11 H19 N O8 CC(=O)N[C@....
9 5KZD Ki = 0.39 mM RCJ C11 H21 N O9 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RCJ; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 HMN 1 1
2 RCJ 1 1
3 WQP 0.6 0.733333
4 SI3 0.568627 0.970588
5 RSH 0.454545 0.647059
6 NGF 0.421053 0.888889
7 MN9 0.403846 0.941176
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KZD; Ligand: RCJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5kzd.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5KZD; Ligand: RCJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5kzd.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5KZD; Ligand: RCJ; Similar sites found: 33
This union binding pocket(no: 3) in the query (biounit: 5kzd.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BOS GLA GAL GLC 0.01001 0.41906 None
2 2BOS GLA GAL GLC NBU 0.01194 0.41414 None
3 2PHX MAN MAN 0.01139 0.41708 2.38095
4 2PHW MAN MAN 0.0172 0.40508 2.38095
5 3C3D FO1 0.01255 0.40719 2.38908
6 2UZH IPE 0.01113 0.41657 3.0303
7 4PQG NAG 0.005617 0.41992 3.07167
8 1P7T PYR 0.001531 0.46389 3.41297
9 1D8C GLV 0.0008654 0.45641 3.41297
10 4K7O EKZ 0.009385 0.41036 3.57143
11 2Z48 NGA 0.00492 0.44485 3.75427
12 2Z48 A2G 0.01271 0.41906 3.75427
13 4EZD SEY 0.01787 0.40075 3.75427
14 2CUN 3PG 0.00476 0.43758 4.09556
15 3K6V CIT 0.009488 0.44342 4.43686
16 1H3F TYE 0.01527 0.41089 4.77816
17 1UJP CIT 0.006061 0.40064 4.79705
18 4IF4 BEF 0.003989 0.43572 4.80769
19 3CV2 OXL 0.01206 0.40979 5.11945
20 2D7I UDP 0.01187 0.40038 5.11945
21 1VKF CIT 0.001037 0.47143 6.91489
22 4L80 OXL 0.007901 0.4266 7.16724
23 4DBH OXL 0.01309 0.41262 7.29167
24 3FGZ BEF 0.003096 0.4353 9.375
25 1L5Y BEF 0.008271 0.41061 10.3226
26 3IP8 B85 0.01174 0.40461 10.8871
27 4BC5 5FX 0.01464 0.40304 11.2628
28 1T9D P22 0.01363 0.41018 11.9454
29 4YG6 GAL NAG 0.02564 0.41142 12.8834
30 1LES GLC FRU 0.01287 0.40654 17.3077
31 3I7S PYR 0.0000009016 0.65019 34.589
32 4PTN GXV 0.001058 0.46738 44.7099
33 1W3T 3GR 0.001425 0.45649 48.1229
Pocket No.: 4; Query (leader) PDB : 5KZD; Ligand: RCJ; 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: 5kzd.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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