Receptor
PDB id Resolution Class Description Source Keywords
2NYR 2.06 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF HUMAN SIRTUIN HOMOLOG 5 IN COMPLEX WITH HOMO SAPIENS HISTONE DEACETYLASE STRUCTURAL GENOMICS STRUCTURAL GENOMICCONSORTIUM SGC HYDROLASE
Ref.: STRUCTURAL BASIS OF INHIBITION OF THE HUMAN NAD+-DE DEACETYLASE SIRT5 BY SURAMIN. STRUCTURE V. 15 377 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SVR B:401;
Valid;
none;
submit data
1297.28 C51 H40 N6 O23 S6 Cc1cc...
ZN A:501;
B:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2NYR 2.06 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF HUMAN SIRTUIN HOMOLOG 5 IN COMPLEX WITH HOMO SAPIENS HISTONE DEACETYLASE STRUCTURAL GENOMICS STRUCTURAL GENOMICCONSORTIUM SGC HYDROLASE
Ref.: STRUCTURAL BASIS OF INHIBITION OF THE HUMAN NAD+-DE DEACETYLASE SIRT5 BY SURAMIN. STRUCTURE V. 15 377 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 2NYR - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
2 4G1C - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 4UTV Ki = 100 uM BEZ GLY VAL LEU LYS GLU TYR GLY VAL FSL n/a n/a
2 2NYR - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
3 4G1C - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 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 4UTV Ki = 100 uM BEZ GLY VAL LEU LYS GLU TYR GLY VAL FSL n/a n/a
6 1M2K - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
7 1M2J - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
8 1M2G - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
9 1ICI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
10 1M2H - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
11 2NYR - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
12 4G1C - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
13 1S7G - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
14 1YC2 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SVR; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 SVR 1 1
2 2NG 0.5 0.796875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NYR; Ligand: SVR; Similar sites found: 59
This union binding pocket(no: 1) in the query (biounit: 2nyr.bio1) has 78 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DCP HBI 0.01546 0.4489 None
2 5XG5 A2G 0.03591 0.42838 None
3 1YP0 PEF 0.04394 0.40428 0.83682
4 2OG2 MLI 0.03064 0.42284 2.21402
5 1KYQ NAD 0.03557 0.41913 2.21402
6 3VYW SAM 0.04007 0.40862 2.21402
7 1D8C SOR 0.01842 0.43801 2.58303
8 3GCZ SAM 0.03503 0.4167 2.58303
9 5X62 SAH 0.0494 0.41165 2.58303
10 5ULP KB1 0.03565 0.40416 2.61194
11 1GQ2 NAP 0.02219 0.40511 2.95203
12 2ZX2 RAM 0.03814 0.44235 3.07692
13 3TDC 0EU 0.003043 0.49621 3.32103
14 1TZD ADP 0.03927 0.43938 3.32103
15 2EG5 SAH 0.02586 0.43263 3.32103
16 3EYA FAD 0.005819 0.41739 3.32103
17 3BIB PSF 0.04418 0.43353 3.44828
18 2AF6 BRU 0.04883 0.43044 3.48837
19 3BP1 GUN 0.0005016 0.53682 3.69004
20 2CXG GLC GLC 0.001676 0.52013 3.69004
21 3VSV XYS 0.02683 0.4448 3.69004
22 5KVA SAM 0.02394 0.4171 3.69004
23 2DPM SAM 0.03199 0.411 3.69004
24 5F90 GLA GAL BGC 5VQ 0.02185 0.44493 3.84615
25 5F90 GLA GAL 0.0225 0.44239 3.84615
26 5GVR LMR 0.02722 0.4313 3.84615
27 4XBA GMP 0.006478 0.46902 4
28 4XBA 5GP 0.01328 0.44823 4
29 1ZQ9 SAM 0.01806 0.43138 4.05904
30 4JOB TLA 0.04533 0.40816 4.05904
31 1LSS NAD 0.02788 0.41903 4.28571
32 5LW0 AR6 0.02621 0.41044 4.329
33 3LL5 IP8 0.02185 0.44906 4.41767
34 4HXY NDP 0.02056 0.4026 4.42804
35 1Q8S MAN MMA 0.02891 0.44677 4.7619
36 1Q8Q MAN MMA 0.03026 0.44563 4.7619
37 1UKG MMA 0.03514 0.43322 4.7619
38 2PHX MAN MAN 0.0492 0.43068 4.7619
39 1QXA GLY GLY GLY 0.03153 0.42887 5.53191
40 2HHP FLC 0.03696 0.44552 5.90406
41 1T9D FAD 0.00437 0.41267 5.90406
42 3T7S SAM 0.04192 0.41269 7.46269
43 2XOD FMN 0.0464 0.40788 7.56302
44 5CDH TLA 0.005348 0.47909 7.74908
45 5UFQ GNP 0.03745 0.40315 8.19672
46 3EGI ADP 0.02574 0.44772 8.73786
47 4JGP PYR 0.02069 0.45491 8.75576
48 1EJ0 SAM 0.04097 0.4132 9.44444
49 1J78 OLA 0.04253 0.43744 10.3321
50 1L3I SAH 0.015 0.41934 10.4167
51 1DJL NAP 0.001653 0.444 10.628
52 1PNO NAP 0.001793 0.45013 11.6667
53 1NBU PH2 0.001861 0.49859 11.7647
54 1D4O NAP 0.0009314 0.47125 11.9565
55 2OOR TXP 0.002046 0.45308 12.069
56 1SQL GUN 0.0004521 0.55183 13.6986
57 5A3B APR 0.00001082 0.558 17.3432
58 2FKA BEF 0.04109 0.42267 27.907
59 3U31 NAD 0.00002077 0.56374 46.1255
Pocket No.: 2; Query (leader) PDB : 2NYR; Ligand: SVR; Similar sites found: 18
This union binding pocket(no: 2) in the query (biounit: 2nyr.bio3) has 74 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KP6 SAL 0.02171 0.41559 None
2 3ML5 AZM 0.01561 0.42351 0.743494
3 3WJO IPE 0.03474 0.40784 1.84502
4 3U1T MLI 0.01818 0.41634 2.58303
5 4XOE KGM 0.04119 0.40068 2.58303
6 5JBX MLI 0.03522 0.40323 3.06513
7 3ZJQ NCA 0.01766 0.42631 3.07692
8 4UXU MLK 0.01849 0.41298 3.21101
9 3P7G MAN 0.02171 0.41504 3.42466
10 1UYY BGC BGC 0.01773 0.41905 3.81679
11 4Y4V DAL 0.04329 0.40906 5.16605
12 4U5I BXP 0.02918 0.40903 5.16605
13 4ZSI GLP 0.01473 0.40365 5.26316
14 1H6H PIB 0.02047 0.40274 6.99301
15 4D1J DGJ 0.02605 0.41263 7.38007
16 2CHT TSA 0.02528 0.4109 7.87402
17 4RDN 6MD 0.005769 0.44475 11.976
18 3UNG ADP 0.03053 0.40547 12.9151
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