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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: 199
This union binding pocket(no: 1) in the query (biounit: 5cx8.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 3W5N RAM 1.0395
2 2CDU FAD 1.10619
3 2PX8 MGT 1.11524
4 2FK8 SAM 1.25786
5 5Y77 FAD 1.2685
6 1GUZ NAD 1.29032
7 5MZI FYK 1.30152
8 4QEK GLC 1.3289
9 4DSG UDP 1.4553
10 4DSG FAD 1.4553
11 4COL DTP 1.4553
12 2WPX ACO 1.47493
13 4RFM 3P6 1.50376
14 2NPX FAD 1.566
15 2NPX NAD 1.566
16 4PJT 2YQ 1.62162
17 2UZ1 TPP 1.6632
18 3IAE D7K 1.6632
19 5OC1 FAD 1.6632
20 2VL8 CTS 1.6632
21 2VL8 UDP 1.6632
22 5ZYN FAD 1.69851
23 2UW1 GVM 1.77515
24 3ZKI WZV 1.81347
25 5I34 GDP 1.81406
26 1Q7E MET 1.86916
27 2CNT COA 1.875
28 1XAJ CRB 1.9774
29 1XAJ NAD 1.9774
30 5AZC PGT 2
31 1YMT DR9 2.03252
32 4QJR PIZ 2.04082
33 1QV1 CZH 2.05128
34 1L1E SAH 2.09059
35 1KPH SAH 2.09059
36 1YP0 PEF 2.09205
37 6B3V 7DQ 2.10526
38 5EEH SAH 2.12766
39 2NUN ADP 2.16718
40 4LH7 NMN 2.16718
41 3A51 VDY 2.18978
42 5BVT PAM 2.23881
43 1XAP TTB 2.24719
44 2LBD REA 2.24719
45 5JKG 6LF 2.2508
46 3QCJ NX4 2.25806
47 3T58 FAD 2.2869
48 4Q0A GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 2.31788
49 5B0I BOG 2.33236
50 1Z44 FMN 2.36686
51 2B82 ADN 2.36967
52 2C29 DQH 2.37389
53 2C29 NAP 2.37389
54 2R2L FPP 2.49377
55 2R2L PB9 2.49377
56 4LHD GLY 2.4948
57 1LTH NAD 2.50784
58 3KPX CZH 2.52525
59 1FCZ 156 2.55319
60 1T27 PCW 2.58303
61 1UHK CZN 2.6178
62 2V1O COA 2.64901
63 3QKT ANP 2.65487
64 1IG3 VIB 2.6616
65 4X6K 3XR 2.7027
66 4YCA NDP 2.72109
67 3D9F N6C 2.73973
68 3D9F FAD 2.73973
69 3QCP FAD 2.76596
70 2OO8 RAJ 2.83912
71 5WIU AQD 2.8436
72 1LDN NAD 2.8481
73 1VLH PNS 2.89017
74 3CLH NAD 2.91545
75 1KUK PCA LYS TRP 2.95567
76 3DCT 064 2.97872
77 4UMJ BFQ 3.04054
78 3RUU 37G 3.05677
79 2OM2 GDP 3.07692
80 5UC9 MYR 3.09735
81 5UQK U2F 3.1185
82 3RZ3 U94 3.27869
83 4MGB XDH 3.52941
84 2FP2 TSA 3.61446
85 1N2X SAM 3.65448
86 4I6G FAD 3.7422
87 3OLL EST 3.75
88 2FV5 541 3.83142
89 3AHQ FAD 3.87097
90 1YQZ FAD 3.88128
91 1BKC INN 3.90625
92 3SUD SUE 3.94089
93 5UC4 83S 4.09091
94 6D6L FY4 4.11765
95 3FAL REA 4.13223
96 3FAL LO2 4.13223
97 4TXI FAD 4.158
98 2D5Z L35 4.25532
99 1RL4 BL5 4.25532
100 4POJ 2VP 4.329
101 4M8E 29V 4.329
102 1OPK MYR 4.3659
103 1R6T TYM 4.40252
104 2DSA GSH 4.4335
105 2DSA HPX 4.4335
106 1GV0 NAD 4.51613
107 1SO2 666 4.52381
108 1H9G COA MYR 4.52675
109 4NVQ SAH 4.5614
110 4NVQ 2OD 4.5614
111 1ZED PNP 4.5738
112 5NWI TYR PHE SER SEP ASN 4.58015
113 4XB4 45D 4.60526
114 5Y02 HBX 4.6729
115 4QJK COA 4.68085
116 1CLU DBG 4.81928
117 1TPY SAH 4.87805
118 4MO2 FDA 4.8913
119 3ZVS MLI 5
120 4WKI 3PW 5.10638
121 4F06 PHB 5.12129
122 3KFC 61X 5.13834
123 3VPH OXM 5.16129
124 4D9C PMP 5.26316
125 3SFI 3SF 5.50847
126 2ZKJ ADP 5.58376
127 5NM7 GLY 5.6391
128 4BQS ADP 5.68182
129 4BQS K2Q 5.68182
130 1CMC SAM 5.76923
131 1KPG SAH 5.92335
132 3KMZ EQO 6.01504
133 3KMR EQN 6.01504
134 4IVG ANP 6.23701
135 4IPE ANP 6.23701
136 1YOK P6L 6.25
137 5X80 SAL 6.25
138 4CDN FAD 6.44491
139 5ZZO FLC 6.46766
140 5K13 6Q7 6.50407
141 1R55 097 6.54206
142 2WAT COA 6.55738
143 3I6I NDP 6.6474
144 1DKF OLA 6.80851
145 1DKF BMS 6.80851
146 1IIM TTP 6.84932
147 1YP1 LYS ASN LEU 6.93069
148 4CRL C1I 7.01754
149 3BQD DAY 7.45098
150 4QVH COA 7.48441
151 3P0K FAD 7.5188
152 1UVC STE 7.69231
153 4TWP AXI 7.74908
154 1ATL 0QI 7.92079
155 2HJR APR 7.92683
156 2FTB OLA 8
157 6CEP NAD 8.08383
158 6CEP OXM 8.08383
159 2QV6 GTP 8.20895
160 3D78 NBB 8.40336
161 2CE7 ADP 8.40336
162 4O4Z N2O 8.44156
163 4OCJ NDG 8.44327
164 2VBU CDP 8.82353
165 2F59 INI 8.9172
166 1VR0 3SL 9.31174
167 4EKQ NPO 9.62567
168 3KP6 SAL 9.93377
169 1RQJ RIS 10.3679
170 5X3R 7Y3 10.7317
171 4E1M TQ2 10.8434
172 4ELG 52J 10.8434
173 4ELG 52I 10.8434
174 2XCM ADP 10.8696
175 4RW3 TDA 10.9272
176 4RW3 PLM 10.9272
177 4UCC ZKW 11.588
178 5V03 658 11.7647
179 5CXI 5TW 11.8227
180 1ELR ACE MET GLU GLU VAL ASP 12.2137
181 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 12.2951
182 3G5S FAD 12.4153
183 5LWY OLB 13.6986
184 2W14 WR2 14.8515
185 3H0A D30 17.2794
186 2YI0 YI0 19.214
187 4OGQ 1O2 20.5882
188 4OGQ 7PH 20.5882
189 3B1M KRC 22.9682
190 4DM8 REA 24
191 2DYS PEK 32.6087
192 5ZCO PEK 32.6087
193 5Z84 CHD 32.6087
194 5Z84 PEK 32.6087
195 2DYR PEK 32.6087
196 5Z84 TGL 32.6087
197 2DYS TGL 32.6087
198 2DYR TGL 32.6087
199 5ZCO TGL 32.6087
Pocket No.: 2; Query (leader) PDB : 5CX8; Ligand: 3DO; Similar sites found with APoc: 13
This union binding pocket(no: 2) in the query (biounit: 5cx8.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 6GBX S77 2.12766
2 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 3.20513
3 3ALG NAG NAG NAG NAG 3.68272
4 5ANU 58T 3.79747
5 3ICS FAD 4.158
6 5XOY LYS 4.55764
7 1E1M FAD 4.56522
8 1E1M NAP 4.56522
9 1W4R TTP 4.61538
10 4EDF UPG 4.7817
11 5X9D 80F 5.59211
12 3CV6 HXS 6.19195
13 2HJ4 PNZ 12.5926
Pocket No.: 3; Query (leader) PDB : 5CX8; Ligand: RP3; Similar sites found with APoc: 59
This union binding pocket(no: 3) in the query (biounit: 5cx8.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 4TQ3 GPP 1.32013
2 1JBW TMF 1.63551
3 1BUC CAA 1.82768
4 2CH5 NDG 2.01729
5 2CH5 NAG 2.01729
6 5V13 JH3 2.08333
7 4NES UDP 2.13904
8 4OKZ 3E9 2.46575
9 2BVL UDP 2.4948
10 2BVL GLC 2.4948
11 1T27 PCW 2.58303
12 3QWB NDP 2.69461
13 4CQ5 TCA 2.7027
14 4XVX P33 FDA 3.08483
15 6FFL GLC GLC GLC 3.09278
16 3F8C HT1 3.1746
17 1QIN GIP 3.27869
18 1XX4 BAM 3.44828
19 5GUE GGS 3.62538
20 4I6G FAD 3.7422
21 1II7 DA 3.9039
22 4GVS F4M 4.11392
23 6CGD GNP 4.2623
24 6CGD AKN 4.2623
25 4I3V NAD 4.3659
26 4NVQ 2OD 4.5614
27 4NVQ SAH 4.5614
28 1N9G NAP 4.92228
29 2II3 CAO 4.96183
30 5N5U 7N8 5.09554
31 4H07 IPH 5.19481
32 5V3Y 5V8 5.24476
33 3F10 8HG 5.47945
34 1FCH TYR GLN SER LYS LEU 5.70652
35 3V66 D3A 5.88235
36 1XW6 GSH 5.9633
37 4H6U ACO 6
38 1YUC EPH 6.27451
39 1ZDU P3A 6.53061
40 2VD9 IN5 6.64962
41 2VD9 EPC 6.64962
42 1SJD NPG 6.79348
43 1JNQ EGT 6.86071
44 3KRO DST 7.79661
45 3KRO IPE 7.79661
46 4QAC KK3 7.8341
47 5WO4 B7V 10.9272
48 6GBV FMN 10.9589
49 3RO7 TDR 12.4528
50 3LDW IPE 12.8788
51 1VG0 GER 17.8744
52 2DYR PGV 32.6087
53 2DYS PGV 32.6087
54 5ZCO PGV 32.6087
55 5Z84 PGV 32.6087
56 5Z84 PEK 32.6087
57 5ZCO PEK 32.6087
58 2DYR PEK 32.6087
59 2DYS PEK 32.6087
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