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Receptor
PDB id Resolution Class Description Source Keywords
2H29 2 Å EC: 2.7.7.18 CRYSTAL STRUCTURE OF NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE FROM STAPHYLOCOCCUS AUREUS: PRODUCT B OUND FORM 1 STAPHYLOCOCCUS AUREUS NADD NAMNAT NMNAT TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE FROM STAPHYLOCCOCUS AUREUS: STRUCTURAL BASIS FOR NAAD INTERACTION IN FUNCTIONAL DIMER. J.MOL.BIOL. V. 360 814 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DND A:998;
B:999;
Valid;
Valid;
none;
none;
submit data
665.418 C21 H27 N6 O15 P2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2H29 2 Å EC: 2.7.7.18 CRYSTAL STRUCTURE OF NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE FROM STAPHYLOCOCCUS AUREUS: PRODUCT B OUND FORM 1 STAPHYLOCOCCUS AUREUS NADD NAMNAT NMNAT TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE FROM STAPHYLOCCOCUS AUREUS: STRUCTURAL BASIS FOR NAAD INTERACTION IN FUNCTIONAL DIMER. J.MOL.BIOL. V. 360 814 2006
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2H29 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 2H2A - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2H29 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 2H2A - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3HFJ ic50 = 36 uM DZ9 C18 H12 F N3 O S2 c1cc(cc(c1....
2 2QTN - NCN C11 H14 N O9 P c1cc(c[n+]....
3 2QTR Kd = 3.2 uM NXX C21 H27 N6 O15 P2 c1cc(c[n+]....
4 3MLB ic50 = 13 uM LJZ C28 H24 Cl2 N6 O4 c1cc(c(cc1....
5 2H29 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 2H2A - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DND; Similar ligands found: 271
No: Ligand ECFP6 Tc MDL keys Tc
1 DND 1 1
2 NXX 1 1
3 NAD 0.765766 0.972603
4 A3D 0.752212 0.959459
5 AMP NAD 0.689655 0.972603
6 A2D 0.659574 0.958904
7 CNA 0.644068 0.972973
8 BA3 0.628866 0.958904
9 B4P 0.622449 0.958904
10 AP5 0.622449 0.958904
11 NHD 0.619835 0.945946
12 ZID 0.619048 0.959459
13 NAP 0.619048 0.959459
14 AR6 0.613861 0.958904
15 APR 0.613861 0.958904
16 NAQ 0.611111 0.910256
17 NA0 0.609375 0.946667
18 ADP 0.606061 0.932432
19 ATP 0.60396 0.932432
20 HEJ 0.60396 0.932432
21 NAE 0.603175 0.934211
22 TAP 0.601562 0.897436
23 AN2 0.6 0.92
24 AT4 0.6 0.896104
25 AQP 0.598039 0.932432
26 5FA 0.598039 0.932432
27 NFD 0.596774 0.922078
28 8ID 0.596639 0.923077
29 CA0 0.594059 0.959459
30 M33 0.594059 0.92
31 OOB 0.592593 0.972603
32 AGS 0.592233 0.884615
33 SAP 0.592233 0.884615
34 AD9 0.592233 0.907895
35 N01 0.592 0.945946
36 OAD 0.590909 0.959459
37 ACP 0.588235 0.907895
38 A1R 0.587156 0.873418
39 DQV 0.581197 0.972603
40 3OD 0.580357 0.959459
41 NDE 0.578947 0.946667
42 A3R 0.572727 0.873418
43 WAQ 0.571429 0.897436
44 NDC 0.57037 0.910256
45 A22 0.568807 0.945946
46 DLL 0.567568 0.972603
47 00A 0.567568 0.922078
48 ACQ 0.566038 0.907895
49 ANP 0.566038 0.907895
50 ADX 0.563107 0.841463
51 9X8 0.5625 0.909091
52 A 0.561224 0.905405
53 AMP 0.561224 0.905405
54 NGD 0.560976 0.923077
55 5AL 0.560748 0.945946
56 ABM 0.56 0.881579
57 NJP 0.56 0.96
58 50T 0.557692 0.894737
59 ATF 0.555556 0.896104
60 PRX 0.552381 0.858974
61 NAJ 0.552 0.945946
62 6YZ 0.550459 0.907895
63 SRP 0.550459 0.921053
64 3UK 0.548673 0.959459
65 4AD 0.544643 0.96
66 AMO 0.544643 0.946667
67 ADQ 0.544643 0.959459
68 B5V 0.54386 0.946667
69 9SN 0.543103 0.910256
70 NAX 0.540984 0.8875
71 FYA 0.53913 0.894737
72 1ZZ 0.53913 0.853659
73 SON 0.538462 0.921053
74 B5M 0.538462 0.934211
75 FA5 0.538462 0.946667
76 GAP 0.537037 0.933333
77 TXE 0.536585 0.922078
78 8QN 0.535714 0.945946
79 F2R 0.535433 0.855422
80 AP2 0.533981 0.896104
81 A12 0.533981 0.896104
82 9JJ 0.533784 0.9
83 48N 0.532787 0.910256
84 PAJ 0.530973 0.898734
85 PR8 0.530435 0.864198
86 NCN 0.53 0.808219
87 TXD 0.528455 0.922078
88 6V0 0.528455 0.910256
89 NAI 0.528455 0.922078
90 AHX 0.526316 0.886076
91 BIS 0.525862 0.873418
92 TXA 0.525862 0.946667
93 YAP 0.525424 0.934211
94 G3A 0.525 0.910256
95 SRA 0.524752 0.858974
96 OMR 0.524194 0.865854
97 APC 0.523364 0.896104
98 TAT 0.522936 0.896104
99 T99 0.522936 0.896104
100 25L 0.521368 0.945946
101 G5P 0.520661 0.910256
102 AU1 0.518868 0.907895
103 LAD 0.517241 0.875
104 ME8 0.512821 0.853659
105 NB8 0.512821 0.910256
106 PTJ 0.512821 0.886076
107 B5Y 0.512605 0.934211
108 LAQ 0.512195 0.853659
109 80F 0.51145 0.878049
110 5SV 0.508772 0.817073
111 9ZD 0.508772 0.897436
112 25A 0.508772 0.932432
113 9ZA 0.508772 0.897436
114 139 0.507812 0.8875
115 RBY 0.504587 0.921053
116 ADP PO3 0.504587 0.931507
117 ADV 0.504587 0.921053
118 GTA 0.504065 0.9
119 NDO 0.503704 0.933333
120 EAD 0.50365 0.8875
121 ALF ADP 0.5 0.860759
122 DAL AMP 0.5 0.945946
123 ADP ALF 0.5 0.860759
124 IOT 0.5 0.823529
125 TYM 0.5 0.946667
126 T5A 0.496124 0.855422
127 AP0 0.496063 0.886076
128 4UU 0.495935 0.934211
129 AFH 0.495935 0.898734
130 XAH 0.495868 0.831325
131 A4P 0.492188 0.835294
132 UP5 0.492063 0.934211
133 4UV 0.491803 0.934211
134 MAP 0.486957 0.884615
135 COD 0.484848 0.804598
136 ADJ 0.484615 0.865854
137 GA7 0.483871 0.896104
138 VO4 ADP 0.482456 0.92
139 ADP VO4 0.482456 0.92
140 DZD 0.481203 0.898734
141 BT5 0.481203 0.823529
142 4UW 0.480315 0.898734
143 TYR AMP 0.479675 0.934211
144 M24 0.477941 0.8875
145 AOC 0.47619 0.789474
146 4TC 0.472868 0.910256
147 YLP 0.472441 0.833333
148 7MD 0.472 0.876543
149 NBP 0.471429 0.898734
150 LMS 0.471154 0.797619
151 MYR AMP 0.471074 0.853659
152 P1H 0.468531 0.865854
153 AMP DBH 0.467742 0.933333
154 A A 0.466667 0.932432
155 ODP 0.466165 0.923077
156 DSZ 0.466102 0.813953
157 A2R 0.465517 0.945946
158 PAP 0.464286 0.918919
159 ATP A A A 0.463415 0.945205
160 NAJ PZO 0.463235 0.886076
161 YLA 0.462121 0.833333
162 YLC 0.461538 0.853659
163 YLB 0.461538 0.833333
164 8X1 0.461538 0.747253
165 NMN 0.461538 0.851351
166 ARG AMP 0.460317 0.843373
167 G5A 0.460177 0.772727
168 5AS 0.458716 0.752809
169 NA7 0.458333 0.896104
170 ADP BMA 0.458333 0.959459
171 AVV 0.457627 0.8625
172 2A5 0.455357 0.858974
173 P5A 0.454545 0.73913
174 VMS 0.452991 0.781609
175 54H 0.452991 0.781609
176 ATR 0.451327 0.905405
177 7D4 0.45045 0.846154
178 ITT 0.45045 0.88
179 UPA 0.450382 0.922078
180 LPA AMP 0.449612 0.853659
181 TSB 0.449153 0.811765
182 A5A 0.448276 0.8
183 AYB 0.447761 0.823529
184 HFD 0.447368 0.884615
185 TAD 0.445312 0.875
186 SSA 0.444444 0.793103
187 6FA 0.442953 0.855422
188 GSU 0.442623 0.793103
189 FB0 0.442177 0.777778
190 AHZ 0.44186 0.853659
191 NSS 0.441667 0.813953
192 0WD 0.441176 0.910256
193 BTX 0.441176 0.811765
194 52H 0.440678 0.772727
195 7D3 0.440367 0.846154
196 5CD 0.44 0.773333
197 8PZ 0.44 0.813953
198 6AD 0.439655 0.851852
199 7MC 0.439394 0.855422
200 9K8 0.439024 0.747253
201 JB6 0.439024 0.873418
202 XYA 0.438776 0.810811
203 RAB 0.438776 0.810811
204 ADN 0.438776 0.810811
205 NVA LMS 0.438017 0.766667
206 5CA 0.436975 0.793103
207 53H 0.436975 0.772727
208 N0B 0.43662 0.855422
209 YSA 0.436508 0.793103
210 A3P 0.436364 0.905405
211 FDA 0.436242 0.825581
212 YLY 0.435714 0.823529
213 LEU LMS 0.434426 0.766667
214 4YB 0.434109 0.795455
215 AF3 ADP 3PG 0.431818 0.875
216 3AT 0.431034 0.906667
217 5N5 0.43 0.786667
218 LSS 0.429752 0.755556
219 NPW 0.42963 0.876543
220 NAJ PYZ 0.429577 0.843373
221 SFD 0.427632 0.747368
222 FAS 0.427632 0.865854
223 FAD 0.427632 0.865854
224 PPS 0.42735 0.819277
225 EP4 0.427184 0.725
226 AR6 AR6 0.426357 0.958904
227 FNK 0.425806 0.797753
228 A4D 0.425743 0.786667
229 DTA 0.423077 0.779221
230 P5F 0.42236 0.858824
231 649 0.421053 0.758242
232 WSA 0.421053 0.802326
233 5X8 0.421053 0.779221
234 3AM 0.420561 0.866667
235 A G 0.42029 0.897436
236 G A A A 0.42029 0.886076
237 4TA 0.42029 0.843373
238 KAA 0.419355 0.747253
239 NDP 0.419118 0.910256
240 MTA 0.419048 0.74359
241 U A G G 0.417266 0.897436
242 F2N 0.417178 0.806818
243 TXP 0.416058 0.910256
244 NZQ 0.416058 0.898734
245 7D5 0.415094 0.820513
246 ARU 0.414634 0.807229
247 6RE 0.412844 0.731707
248 AV2 0.411765 0.857143
249 A A A 0.41129 0.894737
250 3DH 0.411215 0.74359
251 A2P 0.410714 0.891892
252 M2T 0.409524 0.728395
253 SFG 0.408696 0.766234
254 62F 0.407643 0.853659
255 8Q2 0.407407 0.786517
256 DTP 0.40678 0.846154
257 FA9 0.406061 0.855422
258 PUA 0.405594 0.875
259 J7C 0.405405 0.719512
260 A3N 0.405405 0.75641
261 FAY 0.405063 0.876543
262 1DG 0.40411 0.910256
263 DG1 0.40411 0.910256
264 ZAS 0.40367 0.759494
265 RFL 0.402516 0.835294
266 SA8 0.401709 0.722892
267 A5D 0.401709 0.779221
268 U A 0.401408 0.922078
269 SCO 0.401361 0.816092
270 CMX 0.401361 0.816092
271 XNP 0.4 0.864198
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2H29; Ligand: DND; Similar sites found with APoc: 145
This union binding pocket(no: 1) in the query (biounit: 2h29.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 1CEB AMH None
2 1FMB HYB None
3 3ZZQ TRP None
4 1WAP TRP None
5 3ZZS TRP None
6 1QAW TRP None
7 2DQA NAG NAG NAG 0.806452
8 5ZDK ATP 1.0582
9 1FDJ 13P 1.5873
10 1NXJ TLA 1.63934
11 2V5K OXM 1.74216
12 1NHK CMP 2.08333
13 1V47 ADX 2.1164
14 1R6T TYM 2.1164
15 5Z49 RUB 2.1164
16 1R6U TYM 2.1164
17 1JOT GAL A2G 2.25564
18 3LLZ GAL NGA 2.25564
19 2J5B TYE 2.6455
20 4NTO 1PW 2.6455
21 4PZ6 GMP 2.6455
22 1GZF NIR 2.6455
23 4KCF FMN 2.6455
24 6GR0 F8W 2.87356
25 5X3D 7XL 3.125
26 3C8Z 5CA 3.1746
27 1JIL 485 3.1746
28 5C9P FUC 3.1746
29 1RYO OXL 3.1746
30 2V0C LEU LMS 3.1746
31 6BMN PAP 3.1746
32 1G51 AMP 3.1746
33 4GKY MAN 3.44828
34 3C0O M6P 3.7037
35 1JZS MRC 3.7037
36 2XG5 EC2 3.7037
37 2XG5 EC5 3.7037
38 2F9W PAU 3.7037
39 5XET ME8 3.7037
40 2HW1 FRU 3.7037
41 1M1B SPV 3.7037
42 5LNW HG3 3.7037
43 4LYA ATP 3.7037
44 5Y0Q APC 3.7037
45 1W2D ADP 3.7037
46 5W3X ACO 3.7037
47 3NZ1 3NY 3.7037
48 2ZBA COA 3.7037
49 4XH0 ADP 3.7037
50 5Y0N ATP 3.7037
51 4P83 U5P 3.84615
52 2PID YSA 4.2328
53 1PCA CIT 4.2328
54 5O5Y GLC 4.2328
55 3HL4 CDC 4.2328
56 4CNG SAH 4.2328
57 1ZY5 ANP 4.2328
58 5X3R 7Y3 4.2328
59 5O22 C3R 4.2328
60 1POT SPD 4.2328
61 5FPE 3TR 4.2328
62 2BS5 BGC GAL FUC 4.44444
63 4MAF ADX 4.7619
64 1O9U ADZ 4.7619
65 1HV6 MAW MAV GCU 4.7619
66 3KB6 LAC 4.7619
67 4H03 NAD 4.7619
68 3ZRM ZRM 4.7619
69 3AFH GSU 5.29101
70 4J75 TYM 5.29101
71 1J09 GLU 5.29101
72 5OJY CIT 5.29101
73 4YMJ 4EJ 5.29101
74 1J09 ATP 5.29101
75 1DNA CB3 5.29101
76 1TSD F89 5.29101
77 1O6B ADP 5.32544
78 3X1M COA 5.66038
79 3ZIU LSS 5.82011
80 5CIC 51R 5.82011
81 5U5G 7VD 5.82011
82 5LKC FUC GLA A2G 5.82011
83 3HAV SRY 5.82011
84 2DWU DGL 6.15942
85 3AJ4 SEP 6.25
86 5Y0T TAT 6.34921
87 2YY8 MTA 6.34921
88 1A99 PUT 6.34921
89 4NYT PC 6.34921
90 1T0S BML 6.34921
91 3FJG 3PG 6.34921
92 5CLO NS8 6.77966
93 2GKS ADP 6.87831
94 1YID ATP 6.87831
95 3QH2 3NM 6.87831
96 2F6U CIT 7.40741
97 3KFL ME8 7.40741
98 3ND6 ATP 7.60234
99 2X1L ADN 7.93651
100 3COW 52H 7.93651
101 1LCF OXL 7.93651
102 3K9W ADE 8.02139
103 3K9W 4PS 8.02139
104 3UEC ALA ARG TPO LYS 8.21918
105 2X3F APC 8.46561
106 2ZUX RAM 8.46561
107 4BCM T7Z 8.46561
108 1NX0 ALA LYS ALA ILE ALA 8.67052
109 5OD2 GLC 8.99471
110 2BGM MAX 9.35252
111 2QJY UQ2 9.62567
112 4NAT 2W5 10
113 4NAT ADP 10
114 4Y8D 49J 10
115 1N1D C2G 10.0775
116 4K7O EKZ 10.119
117 3UC5 ATP 10.1911
118 2VWT PYR 10.582
119 5O0B 9FE 11.1111
120 1PFY MSP 11.1111
121 1U1J C2F 11.1111
122 6ACS CIT 11.6402
123 5DK4 5BX 11.6402
124 5DK4 ATP 11.6402
125 6E2B PT7 11.8421
126 4DC2 ADE 12.1693
127 3O5N BR0 12.5
128 1F9A ATP 12.5
129 1KQN NAD 12.6984
130 4RL4 PPV 12.6984
131 3TTM PUT 13.2275
132 4TVD BGC 13.2275
133 3N1S 5GP 13.4454
134 5N5U AMP 13.7566
135 5CX6 CDP 13.7566
136 6CHP F0Y 18.0124
137 3ZKN WZV 18.5185
138 1UZ4 IFL 19.0476
139 2C49 ADN 21.164
140 2G36 TRP 21.6931
141 1XF1 CIT 22.7513
142 5ZCO PGV 23.5294
143 1OD6 PNS 31.875
144 1NUS NMN 46.5608
145 1NUS APC 46.5608
Pocket No.: 2; Query (leader) PDB : 2H29; Ligand: DND; Similar sites found with APoc: 29
This union binding pocket(no: 2) in the query (biounit: 2h29.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 3QDU CBS CBS None
2 5VKM GAL SIA 2.6455
3 1P77 ATR 2.6455
4 4BQH 9VU 2.6455
5 1UGW GAL 3.00752
6 1JAC AMG 3.00752
7 1X0P FAD 4.1958
8 5EPO TUD 4.2328
9 1KZL CRM 4.2328
10 4JLS 3ZE 4.60526
11 1IPC MGP 4.7619
12 3HQP ATP 4.7619
13 5H04 NAI 5.29101
14 2IYG FMN 5.64516
15 1TZD ADP 5.82011
16 2X0K PPV 6.34921
17 5JE8 NAD 6.34921
18 1Y7P RIP 7.17489
19 5TDF ADE 7.93651
20 2P6W FLC 7.93651
21 5O0J GLC 8.99471
22 5F7U GLC GLC 8.99471
23 4NC7 I3C 11.1111
24 2QIE 8CS 11.4865
25 1U6R IOM 13.2275
26 1U6R ADP 13.2275
27 3NBK PNS 14.1243
28 2HJR CIT 15.873
29 2H5Z CTO 18.0328
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