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 MORE than expected: % Diff = 2;
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 1256 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 1068 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 922 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: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 F6R 1 1
2 TG6 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 HMS 0.641026 0.972222
8 PA5 0.641026 0.916667
9 5RP 0.641026 0.972222
10 5SP 0.641026 0.972222
11 R10 0.641026 0.916667
12 PAN 0.581395 0.6875
13 M2P 0.555556 0.942857
14 6PG 0.534884 0.916667
15 LG6 0.534884 0.916667
16 TAG 0.5 0.628571
17 FUD 0.5 0.628571
18 LPK 0.5 0.628571
19 LX1 0.5 0.837838
20 SDD 0.5 0.628571
21 PSJ 0.5 0.628571
22 KD0 0.5 0.916667
23 DX5 0.5 0.916667
24 SOL 0.5 0.628571
25 A5P 0.5 0.916667
26 LXP 0.5 0.916667
27 DEZ 0.487805 0.916667
28 S6P 0.487805 0.942857
29 DER 0.487805 0.916667
30 RUB 0.477273 0.916667
31 XBP 0.477273 0.916667
32 DXP 0.47619 0.837838
33 TX4 0.465116 0.645833
34 DG6 0.465116 0.891892
35 R52 0.465116 0.942857
36 R5P 0.465116 0.942857
37 HG3 0.459459 0.805556
38 52L 0.44898 0.702128
39 M6R 0.444444 0.767442
40 AGP 0.444444 0.767442
41 RES 0.444444 0.6875
42 G6Q 0.444444 0.942857
43 4TP 0.431818 0.767442
44 LRY 0.423077 0.733333
45 H4P 0.42 0.790698
46 1NT 0.407407 0.916667
47 E4P 0.404762 0.885714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CX8; Ligand: 3DO; Similar sites found: 5
This union binding pocket(no: 1) in the query (biounit: 5cx8.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ICS FAD 0.04866 0.40231 4.158
2 1E1M FAD 0.02297 0.41726 4.56522
3 1E1M NAP 0.02297 0.41726 4.56522
4 4EDF UPG 0.03228 0.41942 4.7817
5 4F06 PHB 0.0343 0.40716 5.12129
Pocket No.: 2; Query (leader) PDB : 5CX8; Ligand: TG6; Similar sites found: 81
This union binding pocket(no: 2) in the query (biounit: 5cx8.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2CDU FAD 0.01838 0.42085 1.10619
2 2PX8 MGT 0.008339 0.42618 1.11524
3 2FK8 SAM 0.01638 0.40946 1.25786
4 4COL DTP 0.01792 0.40419 1.4553
5 2VL8 CTS 0.01314 0.41264 1.6632
6 2VL8 UDP 0.01411 0.41264 1.6632
7 2UW1 GVM 0.01199 0.40216 1.77515
8 5AZC PGT 0.02257 0.45526 2
9 1YMT DR9 0.02647 0.41801 2.03252
10 4QJR PIZ 0.03263 0.40754 2.04082
11 2NUN ADP 0.0186 0.40796 2.16718
12 3A51 VDY 0.01595 0.40755 2.18978
13 1XAP TTB 0.01451 0.42444 2.24719
14 2LBD REA 0.02081 0.42044 2.24719
15 5JKG 6LF 0.02872 0.42732 2.2508
16 3T58 FAD 0.03868 0.41105 2.2869
17 4IEH 1E9 0.02103 0.41365 2.36686
18 2R2L FPP 0.04772 0.40345 2.49377
19 2R2L PB9 0.04598 0.40345 2.49377
20 4X6K 3XR 0.02561 0.40503 2.7027
21 3QCP FAD 0.01217 0.43366 2.76596
22 4BKJ STI 0.03156 0.40628 2.85714
23 5IR4 ZPE 0.03586 0.41811 2.9106
24 1KUK PCA LYS TRP 0.01327 0.41167 2.95567
25 4UMJ BFQ 0.007951 0.40439 3.04054
26 3RUU 37G 0.01537 0.42242 3.05677
27 3RZ3 U94 0.01653 0.4067 3.27869
28 2FP2 TSA 0.01755 0.41087 3.61446
29 3OLL EST 0.01876 0.40641 3.75
30 2FV5 541 0.02503 0.41358 3.83142
31 1YQZ FAD 0.01028 0.45807 3.88128
32 1BKC INN 0.01058 0.41383 3.90625
33 3FAL LO2 0.03412 0.40742 4.13223
34 3FAL REA 0.02521 0.40445 4.13223
35 1KHT AMP 0.03517 0.40717 4.16667
36 1FBY REA 0.01983 0.41931 4.1841
37 2D5Z L35 0.03271 0.44014 4.25532
38 4M8E 29V 0.0403 0.40137 4.329
39 1SO2 666 0.0223 0.40239 4.52381
40 4XB4 45D 0.0136 0.42548 4.60526
41 4QJK COA 0.01069 0.41927 4.68085
42 1CLU DBG 0.04298 0.41325 4.81928
43 5HCY 60D 0.03358 0.42325 4.83384
44 4MO2 FDA 0.02889 0.4187 4.8913
45 4WKI 3PW 0.01262 0.41239 5.10638
46 3KFC 61X 0.02525 0.4163 5.13834
47 3VPH OXM 0.01663 0.41767 5.16129
48 4D9C PMP 0.0209 0.41964 5.26316
49 1CMC SAM 0.03375 0.4123 5.76923
50 1KPG SAH 0.009664 0.42787 5.92335
51 3KMR EQN 0.02706 0.40098 6.01504
52 1YOK P6L 0.02679 0.42973 6.25
53 5X80 SAL 0.01483 0.40374 6.25
54 5K13 6Q7 0.02265 0.41192 6.50407
55 3I6I NDP 0.03068 0.42622 6.6474
56 1YP1 LYS ASN LEU 0.01005 0.40823 6.93069
57 1L1Q 9DA 0.04039 0.40873 6.98925
58 5APJ 76E 0.01499 0.42238 7.14286
59 3BQD DAY 0.03092 0.40276 7.45098
60 1ATL 0QI 0.01705 0.4204 7.92079
61 2HJR APR 0.01077 0.41624 7.92683
62 2FTB OLA 0.0201 0.42371 8
63 2QV6 GTP 0.03009 0.40889 8.20895
64 4O4Z N2O 0.00485 0.43287 8.44156
65 4OCJ NDG 0.03227 0.40085 8.44327
66 2VBU CDP 0.03851 0.40442 8.82353
67 1VR0 3SL 0.01933 0.40957 9.31174
68 4QJL COA 0.008032 0.43806 10.2128
69 1RQJ RIS 0.02219 0.41839 10.3679
70 2XCM ADP 0.01542 0.41885 10.8696
71 4RW3 TDA 0.001094 0.47403 10.9272
72 4RW3 PLM 0.004499 0.43621 10.9272
73 4UCC ZKW 0.0009698 0.42111 11.588
74 5CXI 5TW 0.01348 0.4221 11.8227
75 3G5S FAD 0.0449 0.40904 12.4153
76 5F1R 42O 0.02467 0.4222 13.0802
77 2W14 WR2 0.01306 0.41245 14.8515
78 3H0A D30 0.04618 0.40052 17.2794
79 3B1M KRC 0.02158 0.41037 22.9682
80 4DM8 REA 0.02729 0.40634 24
81 2DYR PEK 0.01472 0.41805 32.6087
Pocket No.: 3; Query (leader) PDB : 5CX8; Ligand: RP3; Similar sites found: 12
This union binding pocket(no: 3) in the query (biounit: 5cx8.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IEH 1E9 0.02551 0.41578 2.36686
2 4OKZ 3E9 0.02293 0.41465 2.46575
3 4XVX P33 FDA 0.0441 0.4053 3.08483
4 5L2J 6UL 0.03902 0.43724 5.10204
5 5V3Y 5V8 0.01349 0.40483 5.24476
6 1FCH TYR GLN SER LYS LEU 0.02239 0.41607 5.70652
7 1YUC EPH 0.01854 0.41494 6.27451
8 3KRO IPE 0.0163 0.41296 7.79661
9 3KRO DST 0.0163 0.41296 7.79661
10 4ZOM 4Q3 0.02345 0.45056 8.44444
11 3LDW IPE 0.01893 0.42351 12.8788
12 2DYR PEK 0.02078 0.41839 32.6087
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