Receptor
PDB id Resolution Class Description Source Keywords
6SAQ 2.02 Å EC: 1.6.5.11 WILD-TYPE NUOEF FROM AQUIFEX AEOLICUS BOUND TO NADH-OH AQUIFEX AEOLICUS (STRAIN VF5) NADH:UBIQUINONE OXIDOREDUCTASE COMPLEX I ELECTRON TRANSPOR
Ref.: STRUCTURE OF NADH-OH, A NOVEL SPECIFIC INHIBITOR OF RESPIRATORY COMPLEX I TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
L3W D:1003;
B:1003;
Valid;
Valid;
none;
none;
submit data
697.44 C21 H29 N7 O16 P2 c1nc(...
GOL A:1003;
D:1005;
B:1006;
A:1002;
D:1004;
B:1004;
B:1005;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
FES C:1001;
A:1001;
Part of Protein;
Part of Protein;
none;
none;
submit data
175.82 Fe2 S2 S1[Fe...
FMN B:1001;
D:1001;
Valid;
Valid;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
SF4 D:1002;
B:1002;
Part of Protein;
Part of Protein;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6Q9C 1.78 Å EC: 1.6.5.11 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS NADH-QUINONE OXIDOREDU SUBUNITS NUOE AND NUOF BOUND TO NADH UNDER ANAEROBIC CONDIT AQUIFEX AEOLICUS (STRAIN VF5) RESPIRATORY CHAIN COMPLEX I NADH UBIQUINONE OXIDOREDUCTASECLUSTERS OXIDOREDUCTASE
Ref.: A MECHANISM TO PREVENT PRODUCTION OF REACTIVE OXYGE BY ESCHERICHIA COLI RESPIRATORY COMPLEX I. NAT COMMUN V. 10 2551 2019
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6Q9K - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 6SAQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 6HL3 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 6HLM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 6HL4 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 6HLA - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
7 6Q9G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 6Q9J - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 6HLJ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 6Q9C - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 6HL2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 6HLI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6Q9K - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 6SAQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 6HL3 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 6HLM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 6HL4 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 6HLA - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
7 6Q9G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 6Q9J - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 6HLJ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 6Q9C - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 6HL2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 6HLI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6Q9K - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 6SAQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 6HL3 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 6HLM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 6HL4 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 6HLA - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
7 6Q9G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 6Q9J - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 6HLJ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 6Q9C - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 6HL2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 6HLI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: L3W; Similar ligands found: 261
No: Ligand ECFP6 Tc MDL keys Tc
1 L3W 1 1
2 A2D 0.645833 0.932432
3 AR6 0.617647 0.932432
4 APR 0.617647 0.932432
5 BA3 0.616162 0.932432
6 B4P 0.61 0.932432
7 AP5 0.61 0.932432
8 KG4 0.607843 0.933333
9 ADP 0.594059 0.932432
10 HEJ 0.592233 0.932432
11 ATP 0.592233 0.932432
12 AN2 0.588235 0.92
13 AT4 0.588235 0.896104
14 5FA 0.586538 0.932432
15 AQP 0.586538 0.932432
16 CA0 0.582524 0.933333
17 M33 0.582524 0.92
18 AGS 0.580952 0.884615
19 AD9 0.580952 0.907895
20 OAD 0.580357 0.933333
21 HQG 0.577982 0.92
22 ACP 0.576923 0.907895
23 3OD 0.570175 0.933333
24 9X8 0.566372 0.884615
25 5AL 0.564815 0.92
26 ATF 0.559633 0.896104
27 QA7 0.558559 0.884615
28 A22 0.558559 0.92
29 PRX 0.556604 0.858974
30 ANP 0.555556 0.907895
31 ACQ 0.555556 0.907895
32 8LH 0.554545 0.896104
33 ADX 0.552381 0.841463
34 8LE 0.550459 0.884615
35 AMP 0.55 0.905405
36 A 0.55 0.905405
37 48N 0.54918 0.886076
38 A3R 0.548673 0.873418
39 A1R 0.548673 0.873418
40 4AD 0.548673 0.909091
41 50T 0.54717 0.894737
42 8LQ 0.544643 0.896104
43 JNT 0.54386 0.907895
44 BIS 0.543103 0.873418
45 KMQ 0.542373 0.921053
46 6YZ 0.540541 0.907895
47 SRP 0.540541 0.896104
48 8QN 0.539823 0.92
49 ADQ 0.535088 0.907895
50 AMO 0.535088 0.921053
51 WAQ 0.534483 0.873418
52 ABM 0.533981 0.881579
53 45A 0.533981 0.881579
54 DQV 0.532787 0.945946
55 00A 0.530435 0.873418
56 TXA 0.529915 0.921053
57 AMP MG 0.529412 0.891892
58 OMR 0.528 0.843373
59 TXE 0.528 0.947368
60 APC 0.527778 0.896104
61 OOB 0.526316 0.92
62 3UK 0.525862 0.907895
63 AP2 0.52381 0.896104
64 A12 0.52381 0.896104
65 RBY 0.522936 0.896104
66 ADV 0.522936 0.896104
67 V2G 0.522523 0.8625
68 PAJ 0.521739 0.875
69 NAI 0.52 0.973333
70 DND 0.52 0.921053
71 6V0 0.52 0.960526
72 NAX 0.52 0.935897
73 AHX 0.517241 0.886076
74 DLL 0.517241 0.92
75 1ZZ 0.516949 0.831325
76 ME8 0.516949 0.831325
77 NB8 0.516949 0.886076
78 F2R 0.515385 0.833333
79 SRA 0.514563 0.858974
80 ADP BEF 0.514019 0.905405
81 SON 0.514019 0.896104
82 ADP MG 0.514019 0.905405
83 T99 0.513514 0.896104
84 TAT 0.513514 0.896104
85 OZV 0.513043 0.932432
86 5SV 0.513043 0.817073
87 25L 0.512605 0.92
88 AU1 0.509259 0.907895
89 PR8 0.508475 0.841463
90 B5V 0.508475 0.896104
91 LAD 0.508475 0.851852
92 GTA 0.508065 0.853659
93 TXD 0.507937 0.922078
94 DAL AMP 0.504348 0.894737
95 PTJ 0.504202 0.8625
96 80F 0.503759 0.901235
97 9ZD 0.5 0.873418
98 4UU 0.5 0.934211
99 9ZA 0.5 0.873418
100 25A 0.5 0.906667
101 GAP 0.5 0.883117
102 AP0 0.5 0.935065
103 CNA 0.496183 0.921053
104 UP5 0.496063 0.96
105 4UV 0.495935 0.934211
106 9SN 0.495868 0.8625
107 ATP MG 0.495495 0.905405
108 APC MG 0.495495 0.881579
109 ADP PO3 0.495495 0.905405
110 G3A 0.491935 0.886076
111 B5M 0.491803 0.884615
112 B5Y 0.491803 0.884615
113 FA5 0.491803 0.896104
114 ANP MG 0.491228 0.894737
115 BEF ADP 0.491071 0.881579
116 COD 0.488722 0.804598
117 139 0.48855 0.911392
118 AFH 0.488 0.851852
119 G5P 0.488 0.886076
120 XAH 0.487805 0.831325
121 4UW 0.484375 0.898734
122 TYM 0.48062 0.896104
123 LAQ 0.480315 0.831325
124 FYA 0.479339 0.87013
125 MAP 0.478632 0.884615
126 VO4 ADP 0.478261 0.883117
127 ALF ADP 0.478261 0.8375
128 4TC 0.476923 0.935065
129 YLB 0.476923 0.811765
130 YLP 0.476562 0.811765
131 GA7 0.47619 0.871795
132 A2R 0.470085 0.92
133 ADJ 0.466165 0.865854
134 YLC 0.465649 0.853659
135 MYR AMP 0.463415 0.809524
136 LMS 0.462264 0.797619
137 A4P 0.462121 0.879518
138 TAD 0.460938 0.875
139 2A5 0.460177 0.858974
140 IOT 0.458647 0.802326
141 NAD 0.455882 0.92
142 FB0 0.455782 0.777778
143 7D4 0.455357 0.846154
144 JB6 0.455285 0.85
145 T5A 0.455224 0.901235
146 EAD 0.454545 0.935897
147 ARU 0.454545 0.807229
148 UPA 0.454545 0.947368
149 NAQ 0.453901 0.8625
150 ARG AMP 0.453125 0.8
151 BT5 0.452555 0.802326
152 AYB 0.451852 0.802326
153 ADP BMA 0.45082 0.883117
154 LEU LMS 0.45082 0.725275
155 5AS 0.45045 0.752809
156 A3D 0.449275 0.907895
157 AHZ 0.446154 0.809524
158 7D3 0.445455 0.846154
159 VMS 0.445378 0.781609
160 54H 0.445378 0.781609
161 YLA 0.444444 0.833333
162 ATR 0.443478 0.905405
163 PAP 0.443478 0.918919
164 ITT 0.442478 0.88
165 P1H 0.442177 0.9125
166 7MD 0.44186 0.853659
167 TSB 0.441667 0.811765
168 A5A 0.440678 0.8
169 AOC 0.440367 0.813333
170 JSQ 0.439655 0.884615
171 G5A 0.439655 0.772727
172 HFD 0.439655 0.884615
173 NAE 0.43662 0.884615
174 NAJ PZO 0.435714 0.910256
175 P5A 0.435484 0.73913
176 BTX 0.434783 0.811765
177 NSS 0.434426 0.793103
178 ATP A A A 0.433071 0.893333
179 ATP A 0.433071 0.893333
180 EP4 0.432692 0.725
181 6AD 0.432203 0.851852
182 9K8 0.432 0.709677
183 LPA AMP 0.431818 0.809524
184 DZD 0.431655 0.875
185 5CD 0.431373 0.773333
186 NVA LMS 0.430894 0.747253
187 AR6 AR6 0.430769 0.881579
188 ZID 0.430556 0.907895
189 ADN 0.43 0.810811
190 RAB 0.43 0.810811
191 XYA 0.43 0.810811
192 8X1 0.429752 0.747253
193 YLY 0.429577 0.802326
194 NA7 0.427419 0.896104
195 D4F 0.426573 0.831325
196 AVV 0.42623 0.8625
197 5X8 0.426087 0.75641
198 ALF ADP 3PG 0.425373 0.829268
199 AF3 ADP 3PG 0.425373 0.829268
200 SSA 0.425 0.793103
201 MTA 0.424528 0.74359
202 0WD 0.42446 0.960526
203 NAJ PYZ 0.423611 0.865854
204 NDE 0.422819 0.896104
205 DSZ 0.422764 0.793103
206 LSS 0.422764 0.755556
207 7MC 0.422222 0.833333
208 NAD IBO 0.422222 0.906667
209 NAD TDB 0.422222 0.906667
210 5N5 0.421569 0.786667
211 52H 0.421488 0.772727
212 7D5 0.420561 0.820513
213 FNK 0.420382 0.83908
214 M24 0.41958 0.841463
215 6RE 0.418182 0.710843
216 53H 0.418033 0.772727
217 5CA 0.418033 0.793103
218 A4D 0.417476 0.786667
219 ODP 0.417266 0.923077
220 NJP 0.417266 0.909091
221 AV2 0.416667 0.857143
222 3DH 0.416667 0.74359
223 A3P 0.415929 0.905405
224 AMP DBH 0.415385 0.858974
225 DTA 0.415094 0.75641
226 SFG 0.413793 0.74359
227 H1Q 0.413793 0.868421
228 9JJ 0.41358 0.853659
229 V47 0.413223 0.776316
230 NDP 0.413043 0.960526
231 NPW 0.413043 0.924051
232 GSU 0.412698 0.772727
233 N0B 0.410959 0.833333
234 J7C 0.410714 0.719512
235 NO7 0.409836 0.896104
236 ZAS 0.409091 0.7375
237 P5F 0.408537 0.837209
238 PPS 0.408333 0.819277
239 NDC 0.407895 0.8625
240 6MZ 0.40708 0.868421
241 SA8 0.40678 0.702381
242 AMP NAD 0.404255 0.894737
243 A2P 0.403509 0.891892
244 DCA 0.402778 0.795455
245 FDA 0.402597 0.869048
246 62F 0.402516 0.831325
247 M2T 0.401869 0.707317
248 NEC 0.401786 0.74026
249 KAA 0.401575 0.747253
250 J4G 0.401575 0.884615
251 38V 0.401361 0.853659
252 KOY 0.4 0.794872
253 3AT 0.4 0.906667
254 FAY 0.4 0.853659
255 6FA 0.4 0.833333
256 TXP 0.4 0.910256
257 V3L 0.4 0.906667
258 NZQ 0.4 0.948052
259 DTP 0.4 0.846154
260 8PZ 0.4 0.793103
261 3AM 0.4 0.866667
Ligand no: 2; Ligand: FMN; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 9O9 0.574468 0.934211
4 RS3 0.571429 0.831169
5 FAD 0.543307 0.876543
6 FAS 0.543307 0.876543
7 FAE 0.539062 0.865854
8 UBG 0.534351 0.888889
9 5DD 0.475248 0.972603
10 LFN 0.475 0.643836
11 C3F 0.473684 0.74359
12 CF4 0.463918 0.734177
13 FAY 0.446043 0.864198
14 FNR 0.444444 0.909091
15 RFL 0.442857 0.845238
16 4LS 0.411215 0.875
17 1VY 0.406593 0.769231
18 DLZ 0.404494 0.782051
Similar Ligands (3D)
Ligand no: 1; Ligand: L3W; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: FMN; Similar ligands found: 10
No: Ligand Similarity coefficient
1 7O6 0.9670
2 4X4 0.8996
3 4LU 0.8884
4 E2U 0.8865
5 HDF 0.8834
6 AFQ 0.8817
7 E2X 0.8805
8 E89 0.8698
9 1WJ 0.8673
10 FZZ 0.8606
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6Q9C; Ligand: NAI; 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: 6q9c.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6Q9C; Ligand: FMN; 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: 6q9c.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6Q9C; Ligand: NAI; 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: 6q9c.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6Q9C; Ligand: FMN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6q9c.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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