Receptor
PDB id Resolution Class Description Source Keywords
3D4B 1.9 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF SIR2TM IN COMPLEX WITH ACETYL P53 PEPTIDE AND DADME-NAD+ THERMOTOGA MARITIMA ROSSMANN FOLD CYTOPLASM HYDROLASE METAL-BINDING NAD ZINC
Ref.: STRUCTURAL INSIGHTS INTO INTERMEDIATE STEPS IN THE SIR2 DEACETYLATION REACTION. STRUCTURE V. 16 1368 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DZD A:1002;
 Valid;
 none;
 submit data
657.507 C24 H33 N7 O11 P2 c1cc(...
THR SER ARG HIS LYS ALY LEU MET ALA D:6;
 Valid;
 none;
 submit data
1115.37 n/a S(CCC...
ZN A:1001;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4BUZ 1.9 Å EC: 3.5.1.- SIR2 COMPLEX STRUCTURE MIXTURE OF EX-527 INHIBITOR AND REACTION PRODUCTS OR OF REACTION SUBSTRATES P53 PEPTIDE AND THERMOTOGA MARITIMA HYDROLASE NAD-DEPENDENT DEACETYLASE SIRTUIN INHIBITOR COMEX-527 RUNNING REACTION
Ref.: EX-527 INHIBITS SIRTUINS BY EXPLOITING THEIR UNIQUE NAD+-DEPENDENT DEACETYLATION MECHANISM PROC.NATL.ACAD.SCI.USA V. 110 E2772 2013
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 4BUZ - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
2 3D4B - THR SER ARG HIS LYS ALY LEU MET ALA n/a n/a
3 3D81 - SER ARG HIS LYS FZN LEU MET PHE n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 4BUZ - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
2 3D4B - THR SER ARG HIS LYS ALY LEU MET ALA n/a n/a
3 3D81 - SER ARG HIS LYS FZN LEU MET PHE n/a n/a
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 4BUZ - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
2 3D4B - THR SER ARG HIS LYS ALY LEU MET ALA n/a n/a
3 3D81 - SER ARG HIS LYS FZN LEU MET PHE n/a n/a
4 1S5P Kd = 0.44 uM LYS GLY GLY ALA ALY ARG HIS ARG n/a n/a
5 1M2K - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
6 1M2J - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
7 1M2G - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
8 1ICI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
9 1M2H - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
10 6EQS - BV8 C47 H63 N11 O19 P2 S CC(C)NC(=O....
11 2NYR - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
12 6LJN - HIS PHE SER LYS SIN MCM n/a n/a
13 6LJK - BE2 SER ALA ILE LYS SER NIY GLY SET GUA n/a n/a
14 6LJM - SER LEU GLY LYS SIN MCM n/a n/a
15 4G1C - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
16 6FLG Ki = 30.1 nM GZB VAL LEU DQK GLU TYR GLY VAL n/a n/a
17 6ENX - BJW C48 H64 N10 O19 P2 S CC(C)NC(=O....
18 6EO0 - BVT C47 H63 N11 O19 P2 S CC(C)NC(=O....
19 4UTV Kd = 8.2 uM BEZ GLY VAL LEU LYS GLU TYR GLY VAL FSL n/a n/a
20 1S7G - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
21 1YC2 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DZD; Similar ligands found: 215
No: Ligand ECFP6 Tc MDL keys Tc
1 DZD 1 1
2 APC 0.577982 0.923077
3 ADV 0.572727 0.923077
4 RBY 0.572727 0.923077
5 DQV 0.564516 0.922078
6 A12 0.560748 0.923077
7 AP2 0.560748 0.923077
8 OOB 0.547009 0.897436
9 ACP 0.540541 0.910256
10 00A 0.537815 0.853659
11 ACQ 0.535088 0.910256
12 A2D 0.527778 0.909091
13 6YZ 0.521368 0.910256
14 BA3 0.518182 0.909091
15 AU1 0.517857 0.8625
16 M33 0.517857 0.873418
17 CA0 0.517857 0.886076
18 TAD 0.515625 0.901235
19 AMP 0.514019 0.858974
20 A 0.514019 0.858974
21 45A 0.513761 0.8375
22 ABM 0.513761 0.8375
23 B4P 0.513514 0.909091
24 AP5 0.513514 0.909091
25 ADP 0.513514 0.884615
26 KG4 0.513274 0.886076
27 DLL 0.512397 0.897436
28 AMP MG 0.509259 0.846154
29 AN2 0.508929 0.873418
30 AT4 0.508929 0.851852
31 V2G 0.504274 0.888889
32 5AL 0.504274 0.873418
33 B5V 0.504065 0.875
34 9SN 0.504 0.843373
35 CNA 0.503704 0.898734
36 8LQ 0.5 0.875
37 HEJ 0.5 0.884615
38 ATP 0.5 0.884615
39 3UK 0.495935 0.886076
40 SRP 0.495798 0.875
41 APR 0.495652 0.884615
42 AQP 0.495652 0.884615
43 5FA 0.495652 0.884615
44 AR6 0.495652 0.884615
45 WAQ 0.491935 0.9
46 8LE 0.491525 0.841463
47 AD9 0.491379 0.8625
48 AGS 0.491379 0.841463
49 APC MG 0.491379 0.884615
50 ADX 0.491228 0.802326
51 M24 0.489362 0.823529
52 B5M 0.488189 0.864198
53 1ZZ 0.488 0.835294
54 3OD 0.488 0.886076
55 QA7 0.487603 0.841463
56 50T 0.486957 0.85
57 9ZD 0.483607 0.831325
58 9ZA 0.483607 0.831325
59 8LH 0.483333 0.851852
60 GAP 0.483051 0.8625
61 ANP 0.483051 0.8625
62 PRX 0.482759 0.839506
63 SRA 0.481818 0.817073
64 NAX 0.481203 0.86747
65 TXD 0.481203 0.948718
66 DND 0.481203 0.898734
67 PR8 0.48 0.890244
68 A1R 0.479675 0.924051
69 A3R 0.479675 0.924051
70 PAJ 0.479675 0.833333
71 4AD 0.479675 0.8875
72 HQG 0.479339 0.873418
73 LAQ 0.477273 0.835294
74 FA5 0.476562 0.898734
75 B5Y 0.476562 0.864198
76 TXA 0.47619 0.875
77 AHX 0.475806 0.865854
78 ATF 0.475 0.851852
79 NAD 0.47482 0.897436
80 OAD 0.472 0.886076
81 8QN 0.471545 0.873418
82 ADP BEF 0.469565 0.858974
83 ADP MG 0.469565 0.858974
84 SON 0.469565 0.898734
85 LAD 0.468254 0.878049
86 AMO 0.467742 0.898734
87 TXE 0.466667 0.924051
88 ADP PO3 0.466102 0.858974
89 ATP MG 0.466102 0.858974
90 FYA 0.464567 0.897436
91 DAL AMP 0.463415 0.85
92 A22 0.463415 0.897436
93 NAD IBO 0.463235 0.884615
94 NAD TDB 0.463235 0.884615
95 4TC 0.463235 0.9125
96 XAH 0.461538 0.857143
97 MYR AMP 0.460938 0.813953
98 9X8 0.460317 0.841463
99 OZV 0.459677 0.884615
100 6V0 0.459259 0.888889
101 NAI 0.459259 0.876543
102 T99 0.458333 0.851852
103 TAT 0.458333 0.851852
104 A3D 0.457746 0.886076
105 ADQ 0.456 0.886076
106 OMR 0.455882 0.847059
107 Q2P 0.453901 0.755814
108 AMP NAD 0.453901 0.873418
109 NB8 0.453125 0.865854
110 BIS 0.453125 0.831325
111 PTJ 0.453125 0.821429
112 ME8 0.453125 0.835294
113 F0P 0.452555 0.814815
114 JNT 0.452381 0.910256
115 LPA AMP 0.451852 0.813953
116 BT5 0.450704 0.827586
117 BEF ADP 0.45 0.8375
118 5SV 0.448 0.821429
119 25A 0.448 0.884615
120 IOT 0.446043 0.848837
121 TYM 0.445255 0.898734
122 D4F 0.445205 0.813953
123 OZP 0.441176 0.814815
124 4UU 0.440298 0.864198
125 MAP 0.44 0.841463
126 38V 0.439189 0.902439
127 ALF ADP 0.439024 0.797619
128 VO4 ADP 0.439024 0.839506
129 ANP MG 0.439024 0.85
130 AOC 0.438596 0.772152
131 25L 0.438462 0.897436
132 4UW 0.437956 0.833333
133 UP5 0.437956 0.8875
134 80F 0.4375 0.837209
135 4UV 0.43609 0.864198
136 LMS 0.433628 0.761364
137 T5A 0.432624 0.880952
138 ATP A A A 0.431818 0.871795
139 KMQ 0.431818 0.851852
140 ATP A 0.431818 0.871795
141 L3W 0.431655 0.875
142 48N 0.430657 0.865854
143 YLP 0.430657 0.858824
144 ARG AMP 0.42963 0.804598
145 7MD 0.42963 0.879518
146 ZID 0.42953 0.886076
147 NAD CJ3 0.428571 0.788889
148 A3P 0.42735 0.858974
149 G5A 0.42623 0.777778
150 O02 0.42623 0.888889
151 NAE 0.425676 0.864198
152 AMP DBH 0.425373 0.839506
153 EAD 0.423841 0.845238
154 G3A 0.422222 0.865854
155 AP0 0.421429 0.843373
156 52H 0.420635 0.73913
157 KOY 0.42029 0.777778
158 9K8 0.419847 0.697917
159 GA7 0.419118 0.875
160 AFH 0.419118 0.855422
161 G5P 0.419118 0.865854
162 PAP 0.418033 0.871795
163 F2R 0.416667 0.837209
164 NAD BBN 0.416149 0.816092
165 GTA 0.416058 0.835294
166 ADP BMA 0.415385 0.8625
167 COD 0.413793 0.850575
168 NAQ 0.413333 0.843373
169 H1Q 0.413223 0.825
170 AHZ 0.413043 0.772727
171 NDE 0.412903 0.875
172 P1H 0.412903 0.825581
173 V47 0.412698 0.759494
174 139 0.412587 0.890244
175 ADJ 0.412587 0.891566
176 R2V 0.412214 0.764045
177 5AS 0.411765 0.758242
178 7MC 0.411348 0.858824
179 YLB 0.411348 0.858824
180 Q34 0.411348 0.755814
181 YLC 0.411348 0.857143
182 VMS 0.409449 0.747253
183 54H 0.409449 0.747253
184 JB6 0.409091 0.876543
185 A4P 0.408451 0.818182
186 5N5 0.407407 0.769231
187 TSB 0.40625 0.775281
188 8X1 0.40625 0.752688
189 53H 0.40625 0.73913
190 NAJ PZO 0.405405 0.821429
191 A5A 0.404762 0.764045
192 9JJ 0.404762 0.835294
193 LEU LMS 0.40458 0.712766
194 ALF ADP 3PG 0.404255 0.811765
195 N37 0.404255 0.756098
196 BTX 0.40411 0.837209
197 4TA 0.40411 0.847059
198 0WD 0.40411 0.865854
199 A4D 0.40367 0.746835
200 5CD 0.40367 0.734177
201 YLA 0.402778 0.858824
202 XYA 0.401869 0.769231
203 ADN 0.401869 0.769231
204 RAB 0.401869 0.769231
205 DTA 0.401786 0.7625
206 SSA 0.401575 0.777778
207 P5A 0.401515 0.782609
208 7C5 0.40146 0.771084
209 UPA 0.401408 0.876543
210 N0B 0.401316 0.880952
211 LSS 0.4 0.741935
212 8PZ 0.4 0.797753
213 DSZ 0.4 0.777778
214 YLY 0.4 0.848837
215 AYB 0.4 0.848837
Ligand no: 2; Ligand: THR SER ARG HIS LYS ALY LEU MET ALA; Similar ligands found: 65
No: Ligand ECFP6 Tc MDL keys Tc
1 THR SER ARG HIS LYS ALY LEU MET ALA 1 1
2 ARG HIS LYS ALY LEU MET PHE LYS 0.629371 0.84058
3 LYS GLY GLY ALA ALY ARG HIS ARG 0.527027 0.811594
4 ILE LEU MET GLU HIS ILE HIS LYS LEU 0.524138 0.771429
5 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.523179 0.763889
6 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.513514 0.774648
7 ILE LEU ALA LYS PHE LEU HIS ARG LEU 0.509804 0.757143
8 GLY ALA ARG ALA HIS SER SER 0.507353 0.867647
9 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.5 0.855072
10 LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.496774 0.811594
11 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.496689 0.788732
12 ALA LYS PHE ARG HIS ASP 0.48951 0.757143
13 LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.489362 0.794118
14 HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.487342 0.8
15 HIS MET THR GLU VAL VAL ARG HIS CYS 0.484076 0.927536
16 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.483871 0.782609
17 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.483871 0.777778
18 GLU LEU ARG ARG LYS MET MET TYR MET 0.482993 0.788732
19 ACE CSO ARG ALA THR LYS MET LEU 0.482759 0.77027
20 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.48125 0.785714
21 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.47973 0.791045
22 SER ARG ASP HIS SER ARG THR PRO MET 0.479042 0.866667
23 ACE ARG HIS LYS ALY MCM 0.474359 0.716049
24 ARG HIS LYS FDL 0.464516 0.703704
25 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.458599 0.828571
26 ALA ILE LEU HIS ARG LEU LEU GLN 0.456376 0.753623
27 ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP 0.454545 0.865672
28 ACE ARG HIS ALY ALY MCM 0.450331 0.703704
29 THR PHE ALY SER ILE MET LYS 0.448718 0.753623
30 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.448718 0.785714
31 HIS MET THR GLU VAL VAL ARG ARG CYS 0.44586 0.941176
32 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.443709 0.774648
33 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.443038 0.873239
34 ALA SER ASN GLU HIS MET GLU THR MET 0.442953 0.852941
35 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.43871 0.704225
36 GLU LEU LYS ARG LYS MET ILE TYR MET 0.4375 0.763889
37 VAL LEU HIS ASP ASP LEU LEU GLU ALA 0.434783 0.691176
38 PHE ASN GLU LEU SER HIS LEU 0.433824 0.764706
39 ASN ARG LEU MET LEU THR GLY 0.428571 0.808824
40 MET ABA LEU ARG MET THR ALA VAL MET 0.426667 0.794118
41 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.42515 0.84
42 ALA ARG LYS LEU ASP 0.423077 0.691176
43 GLU LEU ASN ARG LYS MET ILE TYR MET 0.422619 0.805556
44 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.422222 0.776119
45 LYS ARG ARG ARG HIS PRO SER GLY 0.421384 0.746667
46 HIS LYS LEU VAL GLN LEU LEU THR THR THR 0.42 0.823529
47 LYS SER HIS GLN GLU 0.41844 0.75
48 MET CYS LEU ARG MET THR ALA VAL MET 0.418301 0.820895
49 HIS HIS ALA SER PRO ARG LYS 0.418182 0.733333
50 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.418182 0.808219
51 SER ARG HIS LYS FZN LEU MET PHE 0.41629 0.683673
52 LYS LYS ARG LEU SER VAL GLU 0.416058 0.746269
53 HIS SER LYS LYS LYS CYS ASP GLU LEU 0.414474 0.838235
54 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 0.413174 0.727273
55 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.412121 0.704225
56 ARG ILE ILE PRO ARG HIS LEU GLN LEU 0.411765 0.736842
57 SER HIS LYS ILE ASP ASN LEU ASP 0.411392 0.811594
58 THR ARG SER GLY ALY VAL MET ARG ARG LEU 0.410959 0.724638
59 SER LEU LYS LEU MET THR THR VAL 0.408759 0.746269
60 SER SER ARG LYS GLU TYR TYR ALA 0.406897 0.671233
61 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.405797 0.75
62 ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR 0.405714 0.888889
63 ARG ARG ALA THR LYS MET NH2 0.402778 0.80597
64 ALA ARG THR GLU LEU TYR ARG SER LEU 0.401274 0.774648
65 ACE ALC ARG ALA MET CY1 SER LEU NH2 0.401235 0.802817
Similar Ligands (3D)
Ligand no: 1; Ligand: DZD; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: THR SER ARG HIS LYS ALY LEU MET ALA; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4BUZ; Ligand: OCZ; 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: 4buz.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4BUZ; Ligand: NAD; 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: 4buz.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4BUZ; Ligand: OAD; 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: 4buz.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
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