Receptor
PDB id Resolution Class Description Source Keywords
4G6H 2.26 Å EC: 1.6.5.9 CRYSTAL STRUCTURE OF NDH WITH NADH SACCHAROMYCES CEREVISIAE ROSSMANN FOLD ELECTRON TRANSFER FAD NADH OXIDOREDUCTASE
Ref.: STRUCTURAL INSIGHT INTO THE TYPE-II MITOCHONDRIAL N DEHYDROGENASES. NATURE V. 491 478 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:601;
B:605;
 Valid;
Valid;
 none;
none;
 submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
MG A:603;
A:604;
A:605;
B:601;
B:602;
B:603;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
NAI A:602;
B:604;
 Valid;
Valid;
 none;
none;
 submit data
665.441 C21 H29 N7 O14 P2 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5YJW 1.85 Å EC: 1.6.5.9 STRUCTURE OF THE NDI1 PROTEIN FROM SACCHAROMYCES CEREVISIAE WITH THE COMPETITIVE INHIBITOR, STIGMATELLIN. SACCHAROMYCES CEREVISIAE (STRAIN ATCC S288C) MONOTOPIC MEMBRANE PROTEIN NUCLEOTIDE-BINDING DOMAIN OXIDO
Ref.: UBIQUINONE BINDING SITE OF YEAST NADH DEHYDROGENASE BY STRUCTURES BINDING NOVEL COMPETITIVE- AND MIXED-INHIBITORS SCI REP V. 8 2427 2018
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4G74 - UQ5 C34 H50 O4 CC1=C(C(=O....
2 4G6G - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4G6H - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
4 5YJW ic50 = 107 nM SMA C30 H42 O7 C/C=C(C)/C....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4G74 - UQ5 C34 H50 O4 CC1=C(C(=O....
2 4G6G - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4G6H - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
4 5YJW ic50 = 107 nM SMA C30 H42 O7 C/C=C(C)/C....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4G74 - UQ5 C34 H50 O4 CC1=C(C(=O....
2 4G6G - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4G6H - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
4 5YJW ic50 = 107 nM SMA C30 H42 O7 C/C=C(C)/C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: FAD; Similar ligands found: 147
No: Ligand ECFP6 Tc MDL keys Tc
1 FAS 1 1
2 FAD 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 UBG 0.845588 0.987654
6 6FA 0.794118 0.987654
7 FAE 0.751773 0.987654
8 SFD 0.651007 0.860215
9 FDA 0.641892 0.906977
10 FNK 0.602564 0.876405
11 JNT 0.598425 0.876543
12 FAJ 0.57485 0.97561
13 62F 0.572327 0.939024
14 F2N 0.566265 0.886364
15 FMN 0.543307 0.876543
16 FA9 0.526316 0.939759
17 6YU 0.516304 0.860215
18 CNV FAD 0.511905 0.908046
19 P6G FDA 0.511628 0.908046
20 FAD NBT 0.508876 0.83871
21 A2D 0.504065 0.875
22 DAL FAD PER 0.491429 0.836957
23 P5F 0.491329 0.941176
24 FAD CNX 0.488506 0.8125
25 APR 0.488372 0.851852
26 AR6 0.488372 0.851852
27 FAD T2C 0.485876 0.819149
28 AGS 0.484615 0.811765
29 M33 0.484375 0.864198
30 BA3 0.484127 0.875
31 ATP 0.48062 0.851852
32 HEJ 0.48062 0.851852
33 B4P 0.480315 0.875
34 ADP 0.480315 0.851852
35 AP5 0.480315 0.875
36 ANP 0.477273 0.831325
37 5FA 0.476923 0.851852
38 AQP 0.476923 0.851852
39 48N 0.469388 0.902439
40 OAD 0.467626 0.876543
41 9X8 0.467626 0.833333
42 FAD NBA 0.467033 0.793814
43 GTA 0.465753 0.892857
44 AT4 0.465116 0.821429
45 AN2 0.465116 0.841463
46 HQG 0.463235 0.841463
47 AD9 0.462121 0.831325
48 3OD 0.460993 0.876543
49 RBF 0.460938 0.790123
50 FB0 0.460606 0.835165
51 139 0.460526 0.858824
52 AP0 0.46 0.835294
53 A22 0.459854 0.864198
54 ACP 0.458015 0.853659
55 8QN 0.456522 0.864198
56 PRX 0.454545 0.831325
57 A3R 0.453237 0.86747
58 A1R 0.453237 0.86747
59 G3A 0.452055 0.902439
60 T5A 0.45098 0.872093
61 G5P 0.44898 0.902439
62 ATF 0.448529 0.821429
63 50T 0.44697 0.819277
64 OZV 0.446043 0.851852
65 6YZ 0.445255 0.853659
66 ACQ 0.444444 0.853659
67 ADQ 0.442857 0.853659
68 PAJ 0.442857 0.847059
69 KMQ 0.441379 0.843373
70 8LE 0.441176 0.855422
71 5AL 0.441176 0.864198
72 ADX 0.439394 0.775281
73 CA0 0.439394 0.853659
74 8LQ 0.438849 0.865854
75 QA7 0.438849 0.855422
76 A4P 0.437909 0.831461
77 25L 0.4375 0.864198
78 P33 FDA 0.436464 0.817204
79 KG4 0.43609 0.853659
80 5SV 0.435714 0.793103
81 8LH 0.434783 0.843373
82 OMR 0.434211 0.818182
83 TXE 0.434211 0.890244
84 45A 0.434109 0.829268
85 ABM 0.434109 0.829268
86 AMP 0.433071 0.82716
87 A 0.433071 0.82716
88 4AD 0.432624 0.855422
89 ADJ 0.432258 0.818182
90 B5M 0.431507 0.878049
91 B5Y 0.431507 0.878049
92 BIS 0.430556 0.802326
93 DJC FAD 0.43 0.827957
94 SRA 0.429688 0.788235
95 AFH 0.42953 0.825581
96 DND 0.427632 0.865854
97 TXD 0.427632 0.890244
98 UP5 0.427632 0.878049
99 6V0 0.427632 0.857143
100 DQV 0.426667 0.8875
101 SRP 0.42446 0.843373
102 PR8 0.423611 0.837209
103 TAT 0.423358 0.821429
104 T99 0.423358 0.821429
105 AMO 0.422535 0.865854
106 PTJ 0.42069 0.835294
107 TXA 0.42069 0.865854
108 FYA 0.42069 0.864198
109 CNA 0.420382 0.865854
110 AHX 0.41958 0.835294
111 00A 0.41958 0.823529
112 AMP MG 0.418605 0.814815
113 MAP 0.41844 0.811765
114 NAI 0.418301 0.845238
115 AU1 0.41791 0.831325
116 A12 0.416667 0.843373
117 AP2 0.416667 0.843373
118 9ZD 0.415493 0.845238
119 25A 0.415493 0.851852
120 9ZA 0.415493 0.845238
121 COD 0.415094 0.842697
122 4TC 0.412903 0.879518
123 APC 0.411765 0.843373
124 ME8 0.410959 0.806818
125 1ZZ 0.410959 0.806818
126 NB8 0.410959 0.835294
127 ADP BEF 0.410448 0.82716
128 ADP MG 0.410448 0.82716
129 DJ0 FAD 0.41 0.865169
130 4UW 0.409091 0.825581
131 NAX 0.409091 0.837209
132 F2R 0.408805 0.850575
133 ADV 0.408759 0.843373
134 RBY 0.408759 0.843373
135 VO4 ADP 0.407143 0.809524
136 P1H 0.405882 0.818182
137 BEF ADP 0.405797 0.807229
138 OOB 0.405594 0.864198
139 LAD 0.40411 0.825581
140 UPA 0.403846 0.86747
141 4UU 0.401316 0.833333
142 GA7 0.401316 0.865854
143 A3D 0.401235 0.876543
144 80F 0.401235 0.808989
145 DLL 0.4 0.864198
146 XAH 0.4 0.806818
147 V2G 0.4 0.857143
Ligand no: 2; Ligand: NAI; Similar ligands found: 287
No: Ligand ECFP6 Tc MDL keys Tc
1 NAI 1 1
2 0WD 0.814815 0.986842
3 NDP 0.803738 0.986842
4 AP0 0.743119 0.961039
5 NMN AMP PO4 0.704348 0.960526
6 NAX 0.663717 0.961538
7 A2D 0.659574 0.933333
8 80F 0.65 0.925926
9 6V0 0.649123 0.986842
10 TXE 0.62931 0.948052
11 BA3 0.628866 0.933333
12 AP5 0.622449 0.933333
13 B4P 0.622449 0.933333
14 TXD 0.62069 0.923077
15 APR 0.613861 0.907895
16 AR6 0.613861 0.907895
17 EAD 0.609375 0.961538
18 AGS 0.607843 0.8625
19 ADP 0.606061 0.907895
20 50T 0.60396 0.871795
21 ATP 0.60396 0.907895
22 HEJ 0.60396 0.907895
23 AT4 0.6 0.873418
24 AN2 0.6 0.896104
25 A22 0.598131 0.921053
26 5FA 0.598039 0.907895
27 AQP 0.598039 0.907895
28 CA0 0.594059 0.909091
29 M33 0.594059 0.896104
30 AD9 0.592233 0.884615
31 NAJ PZO 0.592 0.935897
32 P1H 0.590909 0.9375
33 ACP 0.588235 0.884615
34 KG4 0.588235 0.909091
35 4AD 0.587156 0.886076
36 A1R 0.587156 0.851852
37 PRX 0.582524 0.8375
38 ANP 0.580952 0.884615
39 3OD 0.580357 0.909091
40 SRP 0.579439 0.873418
41 ADX 0.578431 0.821429
42 OAD 0.576577 0.909091
43 5AL 0.575472 0.896104
44 HQG 0.574074 0.896104
45 NAJ PYZ 0.573643 0.890244
46 A3R 0.572727 0.851852
47 ADJ 0.569106 0.890244
48 8LQ 0.568807 0.873418
49 UP5 0.566667 0.960526
50 ACQ 0.566038 0.884615
51 8LH 0.564815 0.873418
52 9X8 0.5625 0.8625
53 A 0.561224 0.881579
54 AMP 0.561224 0.881579
55 8LE 0.560748 0.8625
56 ATF 0.555556 0.873418
57 QA7 0.554545 0.8625
58 JNT 0.553571 0.884615
59 6YZ 0.550459 0.884615
60 8QN 0.54955 0.896104
61 25L 0.547826 0.921053
62 4TC 0.544715 0.935897
63 AMO 0.544643 0.897436
64 ADQ 0.544643 0.909091
65 PAJ 0.544643 0.853659
66 ABM 0.544554 0.858974
67 45A 0.544554 0.858974
68 NPW 0.544 0.949367
69 LAD 0.54386 0.831325
70 PR8 0.54386 0.821429
71 WAQ 0.54386 0.851852
72 DQV 0.541667 0.946667
73 DG1 0.541353 0.986842
74 1DG 0.541353 0.986842
75 AMP MG 0.54 0.868421
76 00A 0.539823 0.875
77 NZQ 0.539683 0.974026
78 1ZZ 0.53913 0.811765
79 BIS 0.53913 0.851852
80 APC 0.537736 0.873418
81 OMR 0.536585 0.823529
82 25A 0.535714 0.907895
83 5SV 0.535714 0.797619
84 OOB 0.535714 0.921053
85 3UK 0.535088 0.909091
86 A12 0.533981 0.873418
87 AP2 0.533981 0.873418
88 B5V 0.530435 0.897436
89 DND 0.528455 0.922078
90 CNA 0.527559 0.922078
91 AHX 0.526316 0.864198
92 DLL 0.526316 0.921053
93 NB8 0.525862 0.864198
94 ME8 0.525862 0.811765
95 PTJ 0.525862 0.841463
96 FYA 0.525862 0.871795
97 KMQ 0.525424 0.897436
98 B5M 0.525424 0.886076
99 SRA 0.524752 0.8375
100 ADP MG 0.52381 0.881579
101 ADP BEF 0.52381 0.881579
102 SON 0.52381 0.873418
103 TAT 0.522936 0.873418
104 T99 0.522936 0.873418
105 OZV 0.522124 0.907895
106 YLP 0.520325 0.793103
107 48N 0.520325 0.864198
108 L3W 0.52 0.973333
109 YLB 0.52 0.793103
110 AU1 0.518868 0.884615
111 ADP PO3 0.518519 0.881579
112 ATP MG 0.518519 0.881579
113 V2G 0.518182 0.841463
114 9SN 0.516949 0.864198
115 BEF ADP 0.513761 0.858974
116 DAL AMP 0.513274 0.871795
117 TXA 0.512821 0.897436
118 FA5 0.512605 0.897436
119 B5Y 0.512605 0.886076
120 GAP 0.509091 0.860759
121 9ZA 0.508772 0.851852
122 9ZD 0.508772 0.851852
123 4UU 0.508197 0.960526
124 YLC 0.507937 0.833333
125 T5A 0.507812 0.925926
126 RBY 0.504587 0.873418
127 APC MG 0.504587 0.858974
128 ADV 0.504587 0.873418
129 4UW 0.504 0.924051
130 TXP 0.503876 0.911392
131 VO4 ADP 0.5 0.860759
132 LAQ 0.5 0.811765
133 TYM 0.5 0.897436
134 G3A 0.5 0.8875
135 F2R 0.5 0.813953
136 ANP MG 0.5 0.871795
137 ALF ADP 0.5 0.817073
138 COD 0.496183 0.786517
139 YLA 0.496124 0.813953
140 139 0.496124 0.9125
141 AFH 0.495935 0.853659
142 G5P 0.495935 0.8875
143 XAH 0.495868 0.811765
144 BT5 0.492424 0.784091
145 AYB 0.492308 0.784091
146 A4P 0.492188 0.880952
147 GTA 0.491935 0.855422
148 4UV 0.491803 0.960526
149 A2R 0.491228 0.896104
150 MAP 0.486957 0.8625
151 XNP 0.484848 0.936709
152 NAD 0.484848 0.921053
153 UPA 0.484375 0.948052
154 7MD 0.483871 0.833333
155 ARG AMP 0.483871 0.781609
156 MYR AMP 0.483333 0.790698
157 NA7 0.483051 0.873418
158 YLY 0.477941 0.784091
159 ATR 0.477477 0.881579
160 ALF ADP 3PG 0.476562 0.809524
161 AOC 0.47619 0.792208
162 ATP A 0.47541 0.894737
163 ATP A A A 0.47541 0.894737
164 BTX 0.473684 0.793103
165 NDP DTT 0.472222 0.902439
166 5AS 0.472222 0.736264
167 GA7 0.472 0.873418
168 LMS 0.471154 0.77907
169 NAQ 0.471014 0.864198
170 LEU LMS 0.470588 0.709677
171 ADP BMA 0.470588 0.884615
172 N0B 0.467626 0.835294
173 A3D 0.466667 0.909091
174 NJP 0.466165 0.910256
175 IOT 0.465649 0.784091
176 AF3 ADP 3PG 0.465116 0.809524
177 PAP 0.464286 0.894737
178 D4F 0.463768 0.833333
179 NAE 0.463768 0.886076
180 NAD TDB 0.461538 0.907895
181 NAD IBO 0.461538 0.907895
182 7MC 0.461538 0.813953
183 H1Q 0.459459 0.846154
184 DZD 0.459259 0.876543
185 ZID 0.457143 0.909091
186 TAD 0.456693 0.853659
187 2A5 0.455357 0.8375
188 62F 0.453947 0.833333
189 AHZ 0.453125 0.790698
190 FB0 0.452055 0.76087
191 JB6 0.45082 0.851852
192 7D4 0.45045 0.825
193 ITT 0.45045 0.857143
194 LPA AMP 0.449612 0.790698
195 G5A 0.447368 0.755556
196 M24 0.446043 0.843373
197 AVV 0.445378 0.841463
198 NDC 0.442177 0.864198
199 NSS 0.441667 0.775281
200 4TA 0.441176 0.890244
201 54H 0.440678 0.764045
202 VMS 0.440678 0.764045
203 7D3 0.440367 0.825
204 5CD 0.44 0.753247
205 PPS 0.439655 0.8
206 XYA 0.438776 0.789474
207 RAB 0.438776 0.789474
208 ADN 0.438776 0.789474
209 NDE 0.438356 0.897436
210 NVA LMS 0.438017 0.731183
211 AR6 AR6 0.4375 0.883117
212 8X1 0.436975 0.731183
213 TSB 0.436975 0.793103
214 53H 0.436975 0.755556
215 DTA 0.436893 0.759494
216 A3P 0.436364 0.881579
217 A2P 0.436364 0.868421
218 A5A 0.435897 0.781609
219 FNK 0.435065 0.840909
220 HFD 0.434783 0.8625
221 JSQ 0.434783 0.8625
222 ODP 0.433824 0.924051
223 SFG 0.433628 0.725
224 Z5A 0.433566 0.858824
225 6FA 0.433333 0.835294
226 SSA 0.432203 0.775281
227 J7C 0.431193 0.702381
228 DTP 0.431034 0.825
229 P5A 0.430894 0.723404
230 AMP NAD 0.430657 0.896104
231 5N5 0.43 0.766234
232 DSZ 0.429752 0.775281
233 LSS 0.429752 0.73913
234 NO7 0.428571 0.873418
235 52H 0.428571 0.755556
236 SFD 0.427632 0.731959
237 9K8 0.427419 0.712766
238 6AD 0.42735 0.831325
239 EP4 0.427184 0.707317
240 FDA 0.426667 0.870588
241 ARU 0.42623 0.788235
242 6RE 0.425926 0.694118
243 A4D 0.425743 0.766234
244 5CA 0.425 0.775281
245 3DH 0.424528 0.725
246 AV2 0.423729 0.835443
247 AMP DBH 0.421875 0.860759
248 5X8 0.421053 0.7375
249 DAT 0.421053 0.825
250 GSU 0.419355 0.755556
251 MTA 0.419048 0.725
252 3AT 0.418803 0.883117
253 ETB 0.41844 0.786517
254 DCA 0.41844 0.777778
255 FAS 0.418301 0.845238
256 FAD 0.418301 0.845238
257 A3N 0.418182 0.759494
258 K3K 0.417323 0.797468
259 F2N 0.417178 0.850575
260 38V 0.416667 0.855422
261 7D5 0.415094 0.8
262 B1U 0.414062 0.734043
263 YSA 0.414062 0.775281
264 NAD BBN 0.412903 0.835294
265 0T1 0.412587 0.777778
266 2AM 0.411215 0.857143
267 K3E 0.410853 0.7875
268 9JJ 0.409938 0.855422
269 M2T 0.409524 0.690476
270 CUU 0.408696 0.883117
271 V47 0.408333 0.779221
272 KAA 0.408 0.731183
273 7C5 0.407692 0.790123
274 3AM 0.407407 0.844156
275 NAP 0.406897 0.909091
276 8PZ 0.40625 0.795455
277 KOY 0.406015 0.797468
278 PUA 0.405594 0.9
279 FAY 0.405063 0.855422
280 P5F 0.404908 0.83908
281 EEM 0.403361 0.670455
282 COA 0.402778 0.777778
283 RFL 0.402516 0.816092
284 GJV 0.401786 0.686047
285 6MZ 0.401786 0.846154
286 SA8 0.401709 0.686047
287 WSA 0.4 0.784091
Similar Ligands (3D)
Ligand no: 1; Ligand: FAD; Similar ligands found: 1
No: Ligand Similarity coefficient
1 FDA T2C 0.8610
Ligand no: 2; Ligand: NAI; Similar ligands found: 4
No: Ligand Similarity coefficient
1 NAJ 0.9967
2 8ID 0.9651
3 NHD 0.9450
4 A7R 0.8646
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5YJW; Ligand: FAD; 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: 5yjw.bio1) has 75 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5YJW; Ligand: FAD; 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: 5yjw.bio1) has 75 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5YJW; Ligand: SMA; 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: 5yjw.bio1) has 78 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5YJW; Ligand: SMA; 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: 5yjw.bio1) has 78 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5YJW; Ligand: SMA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5yjw.bio1) has 77 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5YJW; Ligand: SMA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5yjw.bio1) has 77 residues
No: Leader PDB Ligand Sequence Similarity
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