Receptor
PDB id Resolution Class Description Source Keywords
5CX8 2.4 Å NON-ENZYME: OTHER STRUCTURE OF RAGB, A MAJOR IMMUNODOMINANT VIRULENCE FACTOR O PORPHYROMONAS GINGIVALIS. PORPHYROMONAS GINGIVALIS (STRAIN ATCC W83) MAJOR IMMUNODOMINANT VIRULENCE FACTOR MEMBRANE PROTEIN
Ref.: STRUCTURE OF RAGB, A MAJOR IMMUNODOMINANT OUTER-MEM SURFACE RECEPTOR ANTIGEN OF PORPHYROMONAS GINGIVALI MOL ORAL MICROBIOL V. 31 472 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:606;
A:605;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
RP3 B:601;
Valid;
none;
submit data
214.11 C5 H11 O7 P C1[C@...
GOL A:603;
A:604;
B:602;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
3DO A:601;
Valid;
none;
submit data
164.156 C6 H12 O5 C1[C@...
TG6 A:602;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data
260.136 C6 H13 O9 P C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CX8 2.4 Å NON-ENZYME: OTHER STRUCTURE OF RAGB, A MAJOR IMMUNODOMINANT VIRULENCE FACTOR O PORPHYROMONAS GINGIVALIS. PORPHYROMONAS GINGIVALIS (STRAIN ATCC W83) MAJOR IMMUNODOMINANT VIRULENCE FACTOR MEMBRANE PROTEIN
Ref.: STRUCTURE OF RAGB, A MAJOR IMMUNODOMINANT OUTER-MEM SURFACE RECEPTOR ANTIGEN OF PORPHYROMONAS GINGIVALI MOL ORAL MICROBIOL V. 31 472 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5CX8 - RP3 C5 H11 O7 P C1[C@H](O[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5CX8 - RP3 C5 H11 O7 P C1[C@H](O[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 5CX8 - RP3 C5 H11 O7 P C1[C@H](O[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RP3; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 RP3 1 1
2 1X4 0.487805 0.833333
Ligand no: 2; Ligand: 3DO; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 3DO 1 1
2 2DR 0.483871 0.818182
Ligand no: 3; Ligand: TG6; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 TG6 1 1
2 F6R 1 1
3 I22 0.74359 1
4 2FP 0.7 0.971429
5 P6F 0.7 0.971429
6 P6T 0.7 0.971429
7 5SP 0.641026 0.972222
8 PA5 0.641026 0.916667
9 R10 0.641026 0.916667
10 HMS 0.641026 0.972222
11 5RP 0.641026 0.972222
12 PAN 0.581395 0.6875
13 9C2 0.568182 0.673469
14 GOS 0.555556 0.942857
15 M2P 0.555556 0.942857
16 LG6 0.534884 0.916667
17 6PG 0.534884 0.916667
18 TAG 0.5 0.628571
19 KD0 0.5 0.916667
20 DX5 0.5 0.916667
21 LPK 0.5 0.628571
22 A5P 0.5 0.916667
23 PSJ 0.5 0.628571
24 LXP 0.5 0.916667
25 LX1 0.5 0.837838
26 SOL 0.5 0.628571
27 SDD 0.5 0.628571
28 FUD 0.5 0.628571
29 DER 0.487805 0.916667
30 DEZ 0.487805 0.916667
31 S6P 0.487805 0.942857
32 RUB 0.477273 0.916667
33 XBP 0.477273 0.916667
34 DXP 0.47619 0.837838
35 TX4 0.465116 0.645833
36 R5P 0.465116 0.942857
37 R52 0.465116 0.942857
38 DG6 0.465116 0.891892
39 HG3 0.459459 0.805556
40 52L 0.44898 0.702128
41 G6Q 0.444444 0.942857
42 M6R 0.444444 0.767442
43 RES 0.444444 0.6875
44 AGP 0.444444 0.767442
45 4TP 0.431818 0.767442
46 FQ8 0.425532 0.944444
47 LRY 0.423077 0.733333
48 H4P 0.42 0.790698
49 1NT 0.407407 0.916667
50 E4P 0.404762 0.885714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CX8; Ligand: TG6; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5cx8.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5CX8; Ligand: 3DO; 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: 5cx8.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5CX8; Ligand: RP3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5cx8.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
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