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 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
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 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 (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 221 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 4G1C - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
13 6FLG ic50 = 30.3 nM GZB VAL LEU DQK GLU TYR GLY VAL n/a n/a
14 6ENX - BJW C48 H64 N10 O19 P2 S CC(C)NC(=O....
15 6EO0 - BVT C47 H63 N11 O19 P2 S CC(C)NC(=O....
16 4UTV Ki = 100 uM BEZ GLY VAL LEU LYS GLU TYR GLY VAL FSL n/a n/a
17 1S7G - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
18 1YC2 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DZD; Similar ligands found: 200
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 AP2 0.560748 0.923077
7 A12 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 A 0.514019 0.858974
20 AMP 0.514019 0.858974
21 45A 0.513761 0.8375
22 ABM 0.513761 0.8375
23 AP5 0.513514 0.909091
24 ADP 0.513514 0.884615
25 B4P 0.513514 0.909091
26 KG4 0.513274 0.886076
27 DLL 0.512397 0.897436
28 AN2 0.508929 0.873418
29 AT4 0.508929 0.851852
30 5AL 0.504274 0.873418
31 B5V 0.504065 0.875
32 9SN 0.504 0.843373
33 CNA 0.503704 0.898734
34 HEJ 0.5 0.884615
35 ATP 0.5 0.884615
36 8LQ 0.5 0.875
37 3UK 0.495935 0.886076
38 SRP 0.495798 0.875
39 5FA 0.495652 0.884615
40 AR6 0.495652 0.884615
41 APR 0.495652 0.884615
42 AQP 0.495652 0.884615
43 WAQ 0.491935 0.9
44 8LE 0.491525 0.841463
45 AGS 0.491379 0.841463
46 AD9 0.491379 0.8625
47 APC MG 0.491379 0.884615
48 SAP 0.491379 0.841463
49 ADX 0.491228 0.802326
50 M24 0.489362 0.823529
51 B5M 0.488189 0.864198
52 3OD 0.488 0.886076
53 1ZZ 0.488 0.835294
54 50T 0.486957 0.85
55 9ZD 0.483607 0.831325
56 9ZA 0.483607 0.831325
57 8LH 0.483333 0.851852
58 ANP 0.483051 0.8625
59 GAP 0.483051 0.8625
60 PRX 0.482759 0.839506
61 SRA 0.481818 0.817073
62 DND 0.481203 0.898734
63 NAX 0.481203 0.86747
64 TXD 0.481203 0.948718
65 NXX 0.481203 0.898734
66 PR8 0.48 0.890244
67 4AD 0.479675 0.8875
68 A1R 0.479675 0.924051
69 A3R 0.479675 0.924051
70 PAJ 0.479675 0.833333
71 HQG 0.479339 0.873418
72 LAQ 0.477273 0.835294
73 FA5 0.476562 0.898734
74 B5Y 0.476562 0.864198
75 TXA 0.47619 0.875
76 AHX 0.475806 0.865854
77 ATF 0.475 0.851852
78 NAD 0.47482 0.897436
79 OAD 0.472 0.886076
80 8QN 0.471545 0.873418
81 ADP MG 0.469565 0.858974
82 SON 0.469565 0.898734
83 LAD 0.468254 0.878049
84 AMO 0.467742 0.898734
85 TXE 0.466667 0.924051
86 ATP MG 0.466102 0.858974
87 ADP PO3 0.466102 0.858974
88 YAP 0.465116 0.8875
89 FYA 0.464567 0.897436
90 A22 0.463415 0.897436
91 DAL AMP 0.463415 0.85
92 4TC 0.463235 0.9125
93 XAH 0.461538 0.857143
94 MYR AMP 0.460938 0.813953
95 9X8 0.460317 0.841463
96 OZV 0.459677 0.884615
97 NAI 0.459259 0.876543
98 6V0 0.459259 0.888889
99 TAT 0.458333 0.851852
100 T99 0.458333 0.851852
101 A3D 0.457746 0.886076
102 ADQ 0.456 0.886076
103 OMR 0.455882 0.847059
104 AMP NAD 0.453901 0.873418
105 NB8 0.453125 0.865854
106 BIS 0.453125 0.831325
107 PTJ 0.453125 0.821429
108 ME8 0.453125 0.835294
109 F0P 0.452555 0.814815
110 LPA AMP 0.451852 0.813953
111 BT5 0.450704 0.827586
112 5SV 0.448 0.821429
113 25A 0.448 0.884615
114 VO4 ADP 0.447154 0.85
115 ADP VO4 0.447154 0.85
116 TYR AMP 0.44697 0.864198
117 IOT 0.446043 0.848837
118 TYM 0.445255 0.898734
119 OZP 0.441176 0.814815
120 4UU 0.440298 0.864198
121 MAP 0.44 0.841463
122 ALF ADP 0.439024 0.797619
123 ADP ALF 0.439024 0.797619
124 AOC 0.438596 0.772152
125 25L 0.438462 0.897436
126 4UW 0.437956 0.833333
127 UP5 0.437956 0.8875
128 80F 0.4375 0.837209
129 4UV 0.43609 0.864198
130 A A 0.434109 0.860759
131 LMS 0.433628 0.761364
132 T5A 0.432624 0.880952
133 ATP A 0.431818 0.871795
134 ATP A A A 0.431818 0.871795
135 48N 0.430657 0.865854
136 YLP 0.430657 0.858824
137 7MD 0.42963 0.879518
138 ARG AMP 0.42963 0.804598
139 ZID 0.42953 0.886076
140 A3P 0.42735 0.858974
141 G5A 0.42623 0.777778
142 NAE 0.425676 0.864198
143 AMP DBH 0.425373 0.839506
144 EAD 0.423841 0.845238
145 G3A 0.422222 0.865854
146 AP0 0.421429 0.843373
147 52H 0.420635 0.73913
148 KOY 0.42029 0.777778
149 9K8 0.419847 0.697917
150 AFH 0.419118 0.855422
151 G5P 0.419118 0.865854
152 GA7 0.419118 0.875
153 PAP 0.418033 0.871795
154 F2R 0.416667 0.837209
155 GTA 0.416058 0.835294
156 ADP BMA 0.415385 0.8625
157 COD 0.413793 0.850575
158 NAQ 0.413333 0.843373
159 H1Q 0.413223 0.825
160 AHZ 0.413043 0.772727
161 P1H 0.412903 0.825581
162 NDE 0.412903 0.875
163 ADJ 0.412587 0.891566
164 139 0.412587 0.890244
165 5AS 0.411765 0.758242
166 YLC 0.411348 0.857143
167 YLB 0.411348 0.858824
168 7MC 0.411348 0.858824
169 54H 0.409449 0.747253
170 VMS 0.409449 0.747253
171 JB6 0.409091 0.876543
172 A4P 0.408451 0.818182
173 5N5 0.407407 0.769231
174 TSB 0.40625 0.775281
175 53H 0.40625 0.73913
176 8X1 0.40625 0.752688
177 NAJ PZO 0.405405 0.821429
178 A5A 0.404762 0.764045
179 9JJ 0.404762 0.835294
180 N37 0.404255 0.756098
181 0WD 0.40411 0.865854
182 BTX 0.40411 0.837209
183 4TA 0.40411 0.847059
184 5CD 0.40367 0.734177
185 A4D 0.40367 0.746835
186 YLA 0.402778 0.858824
187 ADN 0.401869 0.769231
188 XYA 0.401869 0.769231
189 RAB 0.401869 0.769231
190 DTA 0.401786 0.7625
191 SSA 0.401575 0.777778
192 P5A 0.401515 0.782609
193 7C5 0.40146 0.771084
194 UPA 0.401408 0.876543
195 N0B 0.401316 0.880952
196 AYB 0.4 0.848837
197 8PZ 0.4 0.797753
198 YLY 0.4 0.848837
199 DSZ 0.4 0.777778
200 LSS 0.4 0.741935
Ligand no: 2; Ligand: THR SER ARG HIS LYS ALY LEU MET ALA; Similar ligands found: 62
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 GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.507143 0.794118
10 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.5 0.855072
11 HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.496732 0.757143
12 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.496689 0.788732
13 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.489796 0.791045
14 ALA LYS PHE ARG HIS ASP 0.48951 0.757143
15 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.483871 0.782609
16 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.483871 0.777778
17 GLU LEU ARG ARG LYS MET MET TYR MET 0.482993 0.788732
18 ACE CSO ARG ALA THR LYS MET LEU 0.482759 0.77027
19 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.48125 0.785714
20 SER ARG ASP HIS SER ARG THR PRO MET 0.479042 0.866667
21 ACE ARG HIS LYS ALY MCM 0.474359 0.716049
22 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.467949 0.828571
23 ARG HIS LYS FDL 0.464516 0.703704
24 ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP 0.464052 0.865672
25 ALA ILE LEU HIS ARG LEU LEU GLN 0.456376 0.753623
26 ACE ARG HIS ALY ALY MCM 0.450331 0.703704
27 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.448718 0.785714
28 THR PHE ALY SER ILE MET LYS 0.448718 0.753623
29 PHE ASN GLU LEU SER HIS LEU 0.444444 0.764706
30 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.443709 0.774648
31 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.443038 0.873239
32 ALA SER ASN GLU HIS MET GLU THR MET 0.442953 0.852941
33 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.43871 0.704225
34 GLU LEU LYS ARG LYS MET ILE TYR MET 0.4375 0.763889
35 VAL LEU HIS ASP ASP LEU LEU GLU ALA 0.434783 0.691176
36 ASN ARG LEU MET LEU THR GLY 0.428571 0.808824
37 THR ARG SER GLY ALY VAL MET ARG ARG LEU 0.427586 0.724638
38 SER HIS MET ALA GLU ILE 0.427481 0.80597
39 MET ABA LEU ARG MET THR ALA VAL MET 0.426667 0.794118
40 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.42515 0.84
41 ALA ARG LYS LEU ASP 0.423077 0.691176
42 GLU LEU ASN ARG LYS MET ILE TYR MET 0.422619 0.805556
43 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.422222 0.776119
44 LYS ARG ARG ARG HIS PRO SER GLY 0.421384 0.746667
45 HIS LYS LEU VAL GLN LEU LEU THR THR THR 0.42 0.823529
46 LYS SER HIS GLN GLU 0.41844 0.75
47 MET CYS LEU ARG MET THR ALA VAL MET 0.418301 0.820895
48 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.418182 0.808219
49 HIS HIS ALA SER PRO ARG LYS 0.418182 0.733333
50 SER SER ARG LYS GLU TYR TYR ALA 0.416667 0.671233
51 SER ARG HIS LYS FZN LEU MET PHE 0.41629 0.683673
52 HIS SER LYS LYS LYS CYS ASP GLU LEU 0.414474 0.838235
53 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 0.413174 0.727273
54 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.412121 0.704225
55 ARG ILE ILE PRO ARG HIS LEU GLN LEU 0.411765 0.736842
56 SER HIS LYS ILE ASP ASN LEU ASP 0.411392 0.811594
57 SER LEU LYS LEU MET THR THR VAL 0.408759 0.746269
58 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.405797 0.75
59 ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR 0.405714 0.888889
60 ARG ARG ALA THR LYS MET NH2 0.402778 0.80597
61 ALA ARG THR GLU LEU TYR ARG SER LEU 0.401274 0.774648
62 ACE ALC ARG ALA MET CY1 SER LEU NH2 0.401235 0.802817
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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