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Receptor
PDB id Resolution Class Description Source Keywords
3QWB 1.59 Å EC: 1.6.5.5 CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE ZETA-CRYSTALLI QUINONE OXIDOREDUCTASE ZTA1 COMPLEXED WITH NADPH SACCHAROMYCES CEREVISIAE ROSSMANN FOLD QUINONE OXIDOREDUCTASES NADPH CYTOPLASM ANDOXIDOREDUCTASE
Ref.: STRUCTURAL INSIGHTS INTO THE COFACTOR-ASSISTED SUBS RECOGNITION OF YEAST QUINONE OXIDOREDUCTASE ZTA1 J.STRUCT.BIOL. V. 176 112 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:336;
A:337;
B:336;
C:336;
D:336;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NDP A:335;
B:335;
C:335;
D:335;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3QWB 1.59 Å EC: 1.6.5.5 CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE ZETA-CRYSTALLI QUINONE OXIDOREDUCTASE ZTA1 COMPLEXED WITH NADPH SACCHAROMYCES CEREVISIAE ROSSMANN FOLD QUINONE OXIDOREDUCTASES NADPH CYTOPLASM ANDOXIDOREDUCTASE
Ref.: STRUCTURAL INSIGHTS INTO THE COFACTOR-ASSISTED SUBS RECOGNITION OF YEAST QUINONE OXIDOREDUCTASE ZTA1 J.STRUCT.BIOL. V. 176 112 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3QWB - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3QWB - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 3JYN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4RVU - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 3QWB - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 1QOR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 172
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 1DG 0.68 1
8 DG1 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 6V0 0.519685 0.974026
25 NAP 0.514493 0.922078
26 7L1 0.507143 0.763441
27 EAD 0.507143 0.949367
28 A2D 0.504673 0.921053
29 TXE 0.503876 0.935897
30 NA0 0.496454 0.910256
31 TXD 0.496124 0.911392
32 SAP 0.495575 0.875
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 PAP 0.482456 0.907895
38 BA3 0.481818 0.921053
39 NAJ PZO 0.478261 0.924051
40 ATP 0.477876 0.921053
41 HEJ 0.477876 0.921053
42 B4P 0.477477 0.921053
43 AP5 0.477477 0.921053
44 ADP 0.477477 0.921053
45 OAD 0.47541 0.897436
46 AR6 0.473684 0.896104
47 AQP 0.473684 0.921053
48 5FA 0.473684 0.921053
49 APR 0.473684 0.896104
50 AN2 0.473214 0.909091
51 3OD 0.467742 0.897436
52 50T 0.464912 0.884615
53 NAJ PYZ 0.464789 0.879518
54 9X8 0.463415 0.851852
55 PO4 PO4 A A A A PO4 0.463415 0.857143
56 V3L 0.461538 0.896104
57 2A5 0.46087 0.85
58 AT4 0.460177 0.886076
59 A1R 0.459016 0.841463
60 4AD 0.459016 0.875
61 ADQ 0.459016 0.897436
62 OVE 0.458716 0.8375
63 OMR 0.458647 0.813953
64 PPS 0.457627 0.811765
65 AD9 0.456897 0.897436
66 CA0 0.45614 0.897436
67 M33 0.45614 0.884615
68 ADJ 0.455882 0.879518
69 A3P 0.455357 0.894737
70 ACP 0.452174 0.897436
71 ENP 0.451613 0.85
72 UP5 0.451128 0.948052
73 SRP 0.45 0.8625
74 ANP 0.449153 0.897436
75 ACQ 0.449153 0.897436
76 PRX 0.448276 0.82716
77 A3R 0.447154 0.841463
78 5AL 0.445378 0.884615
79 7D4 0.443478 0.8375
80 ADX 0.443478 0.811765
81 6YZ 0.438017 0.897436
82 A 0.436364 0.894737
83 AMP 0.436364 0.894737
84 4TC 0.433824 0.924051
85 7D3 0.433628 0.8375
86 DCA 0.433566 0.788889
87 ETB 0.433566 0.797753
88 BIS 0.433071 0.864198
89 1ZZ 0.433071 0.802326
90 00A 0.432 0.864198
91 ATF 0.429752 0.886076
92 DQV 0.428571 0.934211
93 0T1 0.427586 0.788889
94 5SV 0.427419 0.788235
95 8QN 0.427419 0.884615
96 3AM 0.427273 0.857143
97 N01 0.426573 0.884615
98 PR8 0.425197 0.811765
99 LAD 0.425197 0.821429
100 WAQ 0.425197 0.841463
101 DTP 0.425 0.8375
102 AMO 0.424 0.886076
103 PAJ 0.424 0.843373
104 APC 0.423729 0.886076
105 UPA 0.423358 0.935897
106 48N 0.422222 0.853659
107 FYA 0.421875 0.860759
108 PTJ 0.421875 0.853659
109 CNA 0.421429 0.910256
110 PUA 0.42069 0.9125
111 DND 0.419118 0.910256
112 NXX 0.419118 0.910256
113 AV2 0.418033 0.848101
114 COA 0.417808 0.788889
115 3UK 0.417323 0.897436
116 OOB 0.416 0.909091
117 IVC 0.415584 0.78022
118 DAT 0.415254 0.8375
119 NDO 0.414966 0.897436
120 139 0.414286 0.901235
121 B5V 0.414062 0.886076
122 T99 0.413223 0.886076
123 TAT 0.413223 0.886076
124 3AT 0.413223 0.896104
125 YLB 0.413043 0.784091
126 62F 0.4125 0.823529
127 ABM 0.412281 0.848101
128 B5M 0.412214 0.875
129 YAP 0.412214 0.875
130 YLP 0.411765 0.784091
131 NB8 0.410853 0.853659
132 ME8 0.410853 0.802326
133 SON 0.410256 0.886076
134 DLL 0.409449 0.909091
135 AHX 0.409449 0.853659
136 CAO 0.409396 0.763441
137 30N 0.409396 0.72449
138 AMX 0.409396 0.797753
139 COS 0.409396 0.771739
140 7D5 0.409091 0.8125
141 4UW 0.408759 0.9125
142 F2R 0.408451 0.825581
143 APX 0.407692 0.841463
144 SRA 0.40708 0.85
145 CMX 0.406667 0.788889
146 SCO 0.406667 0.788889
147 TYM 0.405797 0.886076
148 COD 0.405594 0.777778
149 CA6 0.405229 0.70297
150 OXK 0.405229 0.771739
151 AP2 0.405172 0.886076
152 A12 0.405172 0.886076
153 9SN 0.40458 0.853659
154 LAQ 0.404412 0.802326
155 T5A 0.404255 0.914634
156 FAM 0.403974 0.771739
157 ACO 0.403974 0.763441
158 FCX 0.403974 0.763441
159 VO4 ADP 0.403226 0.860759
160 ADP VO4 0.403226 0.860759
161 YLC 0.402878 0.823529
162 1VU 0.402597 0.763441
163 B5Y 0.401515 0.875
164 FA5 0.401515 0.886076
165 HAX 0.401316 0.771739
166 AR6 AR6 0.4 0.871795
167 CAJ 0.4 0.771739
168 AFH 0.4 0.843373
169 APU 0.4 0.923077
170 A U 0.4 0.898734
171 TXA 0.4 0.886076
172 4UU 0.4 0.948052
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QWB; Ligand: NDP; Similar sites found with APoc: 214
This union binding pocket(no: 1) in the query (biounit: 3qwb.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1NBU PH2 None
2 1NVT NAP 1.74216
3 1GZ4 ATP 1.79641
4 4IV9 TSR 1.79641
5 1EZ4 NAD 1.88679
6 4JK3 NAD 1.9305
7 4J4H NAI 1.9305
8 4J4H 1J1 1.9305
9 5N2I NAP 2.15517
10 2Z49 AMG 2.39521
11 2Z48 NGA 2.39521
12 3HP9 CF1 2.39521
13 5DN9 NAD 2.39521
14 2Z48 A2G 2.39521
15 2DE4 BPS 2.39521
16 3PTG 932 2.39521
17 4ZGS NAD 2.39521
18 4KYS VIB 2.39521
19 1DSS NAD 2.4024
20 6GIN IR2 2.65781
21 4DDY DN6 2.6616
22 5CEO 50D 2.66667
23 1DLL LAT 2.69461
24 5CX8 RP3 2.69461
25 6AC9 ANP 2.69461
26 4MP8 NAD 2.69461
27 4MP8 MLI 2.69461
28 3V1Y NAD 2.69461
29 2XHK AKG 2.7027
30 5LPB ADP 2.7027
31 4E5N NAD 2.72727
32 1B8U NAD 2.73556
33 2YLN CYS 2.82686
34 5QIN J2V 2.8481
35 3AQT RCO 2.85714
36 4YMJ 4EJ 2.96053
37 3OND ADN 2.99401
38 3OND NAD 2.99401
39 2VYN NAD 3.02115
40 1M1B SPV 3.05085
41 5M67 NAD 3.29341
42 5M67 ADE 3.29341
43 1CT9 AMP 3.29341
44 5M67 3D1 3.29341
45 1DRV A3D 3.2967
46 1CER NAD 3.32326
47 1NCE CB3 3.40909
48 6BMM OLB 3.41297
49 1HYH NAD 3.55987
50 4ARE FLC 3.59281
51 2QJT AMP 3.59281
52 5TE1 7A2 3.59281
53 3NGL NAP 3.62319
54 5OPM DTP 3.89222
55 4BVA NDP 3.89222
56 3NJ4 AFX 3.89222
57 3NJ4 NAD 3.89222
58 3H9E NAD 3.89222
59 3WVR AMP 3.89222
60 1RM0 D6P 3.89222
61 1VM6 NAD 3.94737
62 5GZ6 NDP 3.98773
63 1X7D ORN 4.19162
64 1X7D NAD 4.19162
65 1GQ2 NAP 4.19162
66 5TC4 NAD 4.43038
67 1YS4 NAP 4.49102
68 4PLT OXM 4.53172
69 4PLT NAI 4.53172
70 2VT3 ATP 4.65116
71 5LX9 OLB 4.79042
72 1O0S NAI 4.79042
73 6GH3 M1P 4.79042
74 2D2I NAP 4.79042
75 6BII NAP 4.8048
76 3WB0 FEG 4.81928
77 1GV0 NAD 4.83871
78 2GCG NDP 4.84848
79 5NXX 3Q7 4.85075
80 4WH9 3M8 4.91803
81 2VN9 GVD 4.98339
82 1Q19 SSC 5.08982
83 2HIM ASN 5.08982
84 3CMC NAD 5.08982
85 5C1M CLR 5.6
86 1OIJ AKG 5.64784
87 2NAD NAD 5.68862
88 5A1T NAI 5.68862
89 5A1T OXM 5.68862
90 5AX9 4KT 5.84416
91 1T26 NAI 5.90062
92 1T26 GBD 5.90062
93 3BAZ NAP 5.98802
94 1E3I CXF 5.98802
95 4MDH NAD 5.98802
96 5MDH NAD 6.00601
97 1PZG A3D 6.34441
98 5OJL TXP 6.37584
99 4USI AKG 6.49351
100 3LA3 2FT 6.58436
101 3BJE URA 6.58683
102 5OKL PAM 6.58683
103 4XYB NDP 6.58683
104 1E5Q NDP 6.58683
105 1X9I G6Q 6.62252
106 3HGM ATP 6.80272
107 3I0O SMI 6.88623
108 1LUA NAP 6.96864
109 1OD3 BGC BGC 7.14286
110 3WBF NAP 7.21311
111 5VKT NAP 7.48503
112 5YU3 PRO 7.48503
113 5YU3 NAD 7.48503
114 1PSC EBP 7.48503
115 1BXG NAD 7.78443
116 1C1X NAD 7.78443
117 1F06 NDP 7.8125
118 1F06 2NP 7.8125
119 43CA NPO 7.9646
120 4JX1 CAM 7.9646
121 5U83 ZN8 8.01887
122 1YQD NAP 8.08383
123 5H81 NAP 8.38323
124 5YEC ATP 8.40336
125 1MJH ATP 8.64198
126 1JAY NAP 8.96226
127 4YJK URA 9.12698
128 1P77 ATR 9.19118
129 2GZ3 NAP 9.28144
130 1KOL NAD 9.28144
131 1QAW TRP 9.45946
132 1GR0 NAD 9.58084
133 4URX FK1 9.58084
134 3H8V ATP 9.58904
135 3TD3 GLY 9.7561
136 3ABI NAD 9.88024
137 5EES NAP 10.1215
138 2B5W NAP 10.1796
139 3L6R MLI 10.1796
140 6F3N ADN 10.1796
141 6F3M NAD 10.1796
142 6F3N NAD 10.1796
143 1O6Z NAD 10.231
144 5NUE NAD 10.241
145 2WCU FUC 10.7383
146 2HK9 ATR 10.7784
147 2HK9 NAP 10.7784
148 3QV1 NAD 10.9756
149 5UR0 NAD 11.0778
150 3TWO NDP 11.3772
151 4PLG NAI 11.3772
152 4PLG OXM 11.3772
153 1NVM NAD 11.5385
154 3AXM 6PG 11.6279
155 2DT5 NAD 11.8483
156 3UW4 MAA CHG PRO 0DQ 11.9565
157 1NYT NAP 12.1771
158 6EXS C3H 12.2754
159 2GSD NAD 13.1737
160 4XQC NAD 13.1737
161 1TUK PGM 14.9254
162 1ZEI CRS 15.0943
163 2UVO NDG 15.2047
164 3CIF NAD 15.2695
165 5ZZ6 ADP 15.3846
166 4BCQ TJF 15.6489
167 3BRN SRO 16.5605
168 2ZB4 NAP 16.7665
169 2ZB4 5OP 16.7665
170 2ZJ1 ARJ 17.0659
171 2ZJ1 NAD 17.0659
172 5W97 CHD 17.8082
173 1V8B NAD 20.6587
174 5L95 AMP 21.25
175 2DM6 NAP 21.6216
176 2DM6 IMN 21.6216
177 5YRM BGC GLC 23.2394
178 5YRG BGC GLC 23.2394
179 2ZB3 NDP 23.796
180 1YKF NAP 24.5509
181 5FI3 NAP 25.7703
182 2DFV NAD 27.2455
183 1D1T NAD 28.1437
184 1KEV NDP 28.1437
185 1PL6 NAD 28.7425
186 1U3U BNF 29.0419
187 1U3U NAD 29.0419
188 2FZW NAD 29.4906
189 4RQU NAD 29.6407
190 3GFB NAD 29.6407
191 1F8F NAD 29.9401
192 1P0F NAP 30.2395
193 3WLE NAD 31.3783
194 4WAS NAP 31.4371
195 1N9G NAP 31.4371
196 4Y1B NAP 31.4371
197 4WAS COO 31.4371
198 1CDO NAD 31.7365
199 4B7X NAP 32.0359
200 2JHF NAD 32.6347
201 1LLU NAD 35.3293
202 5O9F NAD 36.2275
203 5O9F 9ON 36.2275
204 5DOZ NDP 36.5269
205 1H2B NAJ 37.1257
206 5DP2 NAP 39.521
207 4IDC 1XX 40.6627
208 4IDC NDP 40.6627
209 4GKV NAD 41.6168
210 4JBI NDP 42.2156
211 4W6Z 8ID 42.8144
212 1R37 NAD 42.9395
213 4A0S NAP 46.4072
214 2J8Z NAP 48.8024
Pocket No.: 2; Query (leader) PDB : 3QWB; Ligand: NDP; Similar sites found with APoc: 37
This union binding pocket(no: 2) in the query (biounit: 3qwb.bio2) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 3BP1 GUN 1.72414
2 2J5V RGP 2.39521
3 1DKU AP2 2.52366
4 3KB6 NAD 2.69461
5 4Z0H NAD 2.69461
6 5Z20 NAI 2.99401
7 6F7X MFU 3.33333
8 1Y13 BIO 3.8674
9 6I6X TLA 3.89222
10 4DPL NAP 3.89222
11 1TE2 PGA 3.9823
12 3WCS MAN NAG 4.72441
13 4D52 GXL 4.7619
14 4CP8 MLI 4.92813
15 5GJH SER ASP PTR MET ASN MET THR PRO 5
16 4XCP PLM 5.29412
17 2XOC ADP 5.36398
18 5EYY MDM 6.12245
19 3AB4 THR 6.17978
20 3I0O ADP 6.88623
21 2DT9 THR 7.78443
22 2FDW D3G 8.38323
23 1ONI BEZ 8.69565
24 1WAP TRP 9.33333
25 5WHU SIA GAL GLC 10.7383
26 3ZZQ TRP 10.7692
27 3ZZS TRP 10.7692
28 1SQL GUN 11.6438
29 2WDQ CBE 11.976
30 1J6W MET 12
31 5UPK ANP 12.5
32 3KO0 TFP 12.8713
33 4P9Z NMI PTR 02K ASN NH2 13.6752
34 5Z84 CHD 17.8082
35 5ZCO CHD 17.8082
36 5YRJ BGC GLC 23.2394
37 2Y69 CHD 24.8062
Pocket No.: 3; Query (leader) PDB : 3QWB; Ligand: NDP; Similar sites found with APoc: 16
This union binding pocket(no: 3) in the query (biounit: 3qwb.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4XJ7 ADE 1.49813
2 1O68 KIV 1.81818
3 2I4O ATP 2.40175
4 1OFL ASG GCD 2.99401
5 1LSS NAD 3.57143
6 3ZUY TCH 4.02477
7 3CF6 SP1 4.19162
8 1HKU NAD 4.19162
9 1Q8P MAN MMA 5.15873
10 2DTJ THR 6.17978
11 1BW9 NAD 7.78443
12 1PVS 7HP 7.80142
13 1RL4 BRR 7.97872
14 4F9C 0SX 10.4167
15 3D04 SAK 12.5786
16 2XRH NIO 14
Pocket No.: 4; Query (leader) PDB : 3QWB; Ligand: NDP; Similar sites found with APoc: 11
This union binding pocket(no: 4) in the query (biounit: 3qwb.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 5DMZ ADP 1.49701
2 6CZY PMP 2.69461
3 1GAD NAD 3.0303
4 6A56 LAT 4.26829
5 1P0Z FLC 5.34351
6 1C1X HFA 7.78443
7 4M5P MLA 9.28144
8 4JN6 OXL 9.88024
9 2HK9 SKM 10.7784
10 1PWB GLC 11.2994
11 4C2W ANP 11.5385
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