Receptor
PDB id Resolution Class Description Source Keywords
4Y9D 2.01 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF LIGD IN COMPLEX WITH NADH FROM SPHINGOB STRAIN SYK-6 SPHINGOBIUM SP. SYK-6 SHORT CHAIN DEHYDROGENASE/REDUCTASE SDR FAMILY OXIDOREDUCTA
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE LATE ENZYMES IN THE LIGNIN BETA-ARYL ETHER CLEAVAGE FROM SPHINGOBIUM SP. SYK-6. J.BIOL.CHEM. V. 291 10228 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAI A:401;
 Valid;
 Atoms found LESS than expected: % Diff = 0;
 submit data
665.441 C21 H29 N7 O14 P2 c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4Y9D 2.01 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF LIGD IN COMPLEX WITH NADH FROM SPHINGOB STRAIN SYK-6 SPHINGOBIUM SP. SYK-6 SHORT CHAIN DEHYDROGENASE/REDUCTASE SDR FAMILY OXIDOREDUCTA
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE LATE ENZYMES IN THE LIGNIN BETA-ARYL ETHER CLEAVAGE FROM SPHINGOBIUM SP. SYK-6. J.BIOL.CHEM. V. 291 10228 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 318 families.
1 4Y9D - NAI C21 H29 N7 O14 P2 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 280 families.
1 4Y9D - NAI C21 H29 N7 O14 P2 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 4YAC - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
2 4Y9D - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
3 4YAI - GGE C17 H20 O6 COc1ccccc1....
4 4YAG - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAI; Similar ligands found: 262
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 AR6 0.613861 0.907895
16 APR 0.613861 0.907895
17 EAD 0.609375 0.961538
18 SAP 0.607843 0.8625
19 AGS 0.607843 0.8625
20 ADP 0.606061 0.907895
21 HEJ 0.60396 0.907895
22 50T 0.60396 0.871795
23 ATP 0.60396 0.907895
24 AN2 0.6 0.896104
25 AT4 0.6 0.873418
26 A22 0.598131 0.921053
27 AQP 0.598039 0.907895
28 5FA 0.598039 0.907895
29 M33 0.594059 0.896104
30 CA0 0.594059 0.909091
31 AD9 0.592233 0.884615
32 NAJ PZO 0.592 0.935897
33 P1H 0.590909 0.9375
34 ACP 0.588235 0.884615
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 NAJ PYZ 0.573643 0.890244
45 A3R 0.572727 0.851852
46 ADJ 0.569106 0.890244
47 UP5 0.566667 0.960526
48 ACQ 0.566038 0.884615
49 9X8 0.5625 0.8625
50 A 0.561224 0.881579
51 AMP 0.561224 0.881579
52 ATF 0.555556 0.873418
53 6YZ 0.550459 0.884615
54 8QN 0.54955 0.896104
55 25L 0.547826 0.921053
56 4TC 0.544715 0.935897
57 AMO 0.544643 0.897436
58 PAJ 0.544643 0.853659
59 ADQ 0.544643 0.909091
60 ABM 0.544554 0.858974
61 NPW 0.544 0.949367
62 WAQ 0.54386 0.851852
63 LAD 0.54386 0.831325
64 PR8 0.54386 0.821429
65 DQV 0.541667 0.946667
66 DG1 0.541353 0.986842
67 1DG 0.541353 0.986842
68 00A 0.539823 0.875
69 NZQ 0.539683 0.974026
70 BIS 0.53913 0.851852
71 1ZZ 0.53913 0.811765
72 APC 0.537736 0.873418
73 OMR 0.536585 0.823529
74 OOB 0.535714 0.921053
75 25A 0.535714 0.907895
76 5SV 0.535714 0.797619
77 3UK 0.535088 0.909091
78 A12 0.533981 0.873418
79 AP2 0.533981 0.873418
80 B5V 0.530435 0.897436
81 DND 0.528455 0.922078
82 NXX 0.528455 0.922078
83 CNA 0.527559 0.922078
84 DLL 0.526316 0.921053
85 AHX 0.526316 0.864198
86 PTJ 0.525862 0.841463
87 ME8 0.525862 0.811765
88 FYA 0.525862 0.871795
89 NB8 0.525862 0.864198
90 B5M 0.525424 0.886076
91 YAP 0.525424 0.886076
92 SRA 0.524752 0.8375
93 SON 0.52381 0.873418
94 TAT 0.522936 0.873418
95 T99 0.522936 0.873418
96 ADP VO4 0.522523 0.871795
97 VO4 ADP 0.522523 0.871795
98 48N 0.520325 0.864198
99 YLP 0.520325 0.793103
100 YLB 0.52 0.793103
101 AU1 0.518868 0.884615
102 ADP PO3 0.518519 0.881579
103 9SN 0.516949 0.864198
104 DAL AMP 0.513274 0.871795
105 TXA 0.512821 0.897436
106 B5Y 0.512605 0.886076
107 FA5 0.512605 0.897436
108 GAP 0.509091 0.860759
109 9ZA 0.508772 0.851852
110 9ZD 0.508772 0.851852
111 4UU 0.508197 0.960526
112 YLC 0.507937 0.833333
113 T5A 0.507812 0.925926
114 RBY 0.504587 0.873418
115 ADV 0.504587 0.873418
116 TYR AMP 0.504132 0.8625
117 4UW 0.504 0.924051
118 TXP 0.503876 0.911392
119 ALF ADP 0.5 0.817073
120 G3A 0.5 0.8875
121 F2R 0.5 0.813953
122 TYM 0.5 0.897436
123 ADP ALF 0.5 0.817073
124 LAQ 0.5 0.811765
125 COD 0.496183 0.786517
126 139 0.496124 0.9125
127 YLA 0.496124 0.813953
128 G5P 0.495935 0.8875
129 AFH 0.495935 0.853659
130 XAH 0.495868 0.811765
131 BT5 0.492424 0.784091
132 AYB 0.492308 0.784091
133 A4P 0.492188 0.880952
134 GTA 0.491935 0.855422
135 4UV 0.491803 0.960526
136 A2R 0.491228 0.896104
137 MAP 0.486957 0.8625
138 NAD 0.484848 0.921053
139 XNP 0.484848 0.936709
140 UPA 0.484375 0.948052
141 7MD 0.483871 0.833333
142 ARG AMP 0.483871 0.781609
143 MYR AMP 0.483333 0.790698
144 NA7 0.483051 0.873418
145 YLY 0.477941 0.784091
146 ATR 0.477477 0.881579
147 AOC 0.47619 0.792208
148 ATP A A A 0.47541 0.894737
149 BTX 0.473684 0.793103
150 5AS 0.472222 0.736264
151 GA7 0.472 0.873418
152 LMS 0.471154 0.77907
153 NAQ 0.471014 0.864198
154 ADP BMA 0.470588 0.884615
155 N0B 0.467626 0.835294
156 A A 0.466667 0.883117
157 A3D 0.466667 0.909091
158 NJP 0.466165 0.910256
159 IOT 0.465649 0.784091
160 AF3 ADP 3PG 0.465116 0.809524
161 PAP 0.464286 0.894737
162 NAE 0.463768 0.886076
163 7MC 0.461538 0.813953
164 DZD 0.459259 0.876543
165 ZID 0.457143 0.909091
166 TAD 0.456693 0.853659
167 2A5 0.455357 0.8375
168 62F 0.453947 0.833333
169 AHZ 0.453125 0.790698
170 FB0 0.452055 0.76087
171 JB6 0.45082 0.851852
172 ITT 0.45045 0.857143
173 7D4 0.45045 0.825
174 LPA AMP 0.449612 0.790698
175 G5A 0.447368 0.755556
176 LEU LMS 0.446281 0.731183
177 M24 0.446043 0.843373
178 AVV 0.445378 0.841463
179 NDC 0.442177 0.864198
180 NSS 0.441667 0.775281
181 4TA 0.441176 0.890244
182 VMS 0.440678 0.764045
183 54H 0.440678 0.764045
184 7D3 0.440367 0.825
185 5CD 0.44 0.753247
186 PPS 0.439655 0.8
187 XYA 0.438776 0.789474
188 ADN 0.438776 0.789474
189 RAB 0.438776 0.789474
190 NDE 0.438356 0.897436
191 NVA LMS 0.438017 0.731183
192 AR6 AR6 0.4375 0.883117
193 TSB 0.436975 0.793103
194 53H 0.436975 0.755556
195 8X1 0.436975 0.731183
196 DTA 0.436893 0.759494
197 A2P 0.436364 0.868421
198 A3P 0.436364 0.881579
199 A5A 0.435897 0.781609
200 FNK 0.435065 0.840909
201 HFD 0.434783 0.8625
202 ODP 0.433824 0.924051
203 SFG 0.433628 0.725
204 Z5A 0.433566 0.858824
205 6FA 0.433333 0.835294
206 SSA 0.432203 0.775281
207 J7C 0.431193 0.702381
208 DTP 0.431034 0.825
209 P5A 0.430894 0.723404
210 AMP NAD 0.430657 0.896104
211 5N5 0.43 0.766234
212 DSZ 0.429752 0.775281
213 LSS 0.429752 0.73913
214 52H 0.428571 0.755556
215 SFD 0.427632 0.731959
216 9K8 0.427419 0.712766
217 6AD 0.42735 0.831325
218 EP4 0.427184 0.707317
219 FDA 0.426667 0.870588
220 ARU 0.42623 0.788235
221 6RE 0.425926 0.694118
222 A4D 0.425743 0.766234
223 5CA 0.425 0.775281
224 3DH 0.424528 0.725
225 AV2 0.423729 0.835443
226 AMP DBH 0.421875 0.860759
227 U A 0.421429 0.923077
228 DAT 0.421053 0.825
229 5X8 0.421053 0.7375
230 GSU 0.419355 0.755556
231 MTA 0.419048 0.725
232 3AT 0.418803 0.883117
233 ETB 0.41844 0.786517
234 DCA 0.41844 0.777778
235 FAD 0.418301 0.845238
236 FAS 0.418301 0.845238
237 A3N 0.418182 0.759494
238 F2N 0.417178 0.850575
239 7D5 0.415094 0.8
240 A U 0.414815 0.910256
241 YSA 0.414062 0.775281
242 0T1 0.412587 0.777778
243 A C A C 0.411348 0.8875
244 2AM 0.411215 0.857143
245 9JJ 0.409938 0.855422
246 M2T 0.409524 0.690476
247 KAA 0.408 0.731183
248 7C5 0.407692 0.790123
249 3AM 0.407407 0.844156
250 NAP 0.406897 0.909091
251 8PZ 0.40625 0.795455
252 PUA 0.405594 0.9
253 FAY 0.405063 0.855422
254 P5F 0.404908 0.83908
255 EEM 0.403361 0.670455
256 COA 0.402778 0.777778
257 RFL 0.402516 0.816092
258 GJV 0.401786 0.686047
259 SA8 0.401709 0.686047
260 U A C C 0.401408 0.898734
261 WSA 0.4 0.784091
262 G A A A 0.4 0.841463
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4Y9D; Ligand: NAI; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 4y9d.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5BJX NAD 12.7869
2 5BJX UDP 12.7869
3 3ZV6 4HB 28.8256
4 3ZV6 NAD 28.8256
5 5O42 9JW 30.6569
6 5O42 BGC 30.6569
7 5O42 NAD 30.6569
Pocket No.: 2; Query (leader) PDB : 4Y9D; 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: 2) in the query (biounit: 4y9d.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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