Receptor
PDB id Resolution Class Description Source Keywords
3q9b 2.25 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF APAH COMPLEXED WITH M344 MYCOPLANA RAMOSA HDAC POLYAMINES ARGINASE FOLD DEACETYLASE HYDROLASE-HYDRINHIBITOR COMPLEX
Ref.: STRUCTURE OF PROKARYOTIC POLYAMINE DEACETYLASE REVE EVOLUTIONARY FUNCTIONAL RELATIONSHIPS WITH EUKARYOT HISTONE DEACETYLASES . BIOCHEMISTRY V. 50 1808 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B3N A:401;
B:407;
C:401;
D:407;
E:401;
F:407;
G:401;
H:407;
I:401;
J:407;
K:401;
L:407;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
307.388 C16 H25 N3 O3 CN(C)...
DMS A:342;
A:403;
A:405;
A:411;
A:413;
A:415;
A:417;
A:419;
A:421;
A:423;
B:342;
B:403;
B:405;
B:411;
B:413;
B:415;
B:417;
B:419;
B:423;
C:405;
C:411;
C:415;
C:419;
C:421;
C:423;
D:342;
D:343;
D:403;
D:405;
D:411;
D:413;
D:415;
D:417;
D:419;
D:421;
D:423;
E:342;
E:403;
E:405;
E:411;
E:413;
E:415;
E:417;
E:419;
E:421;
E:423;
F:342;
F:343;
F:344;
F:405;
F:411;
F:413;
F:415;
F:417;
F:419;
F:421;
F:423;
G:342;
G:343;
G:403;
G:405;
G:411;
G:413;
G:415;
G:417;
G:419;
G:423;
H:405;
H:411;
H:413;
H:415;
H:417;
H:419;
H:421;
H:423;
I:405;
I:411;
I:413;
I:415;
I:417;
I:419;
I:421;
I:423;
J:403;
J:405;
J:413;
J:415;
J:417;
J:419;
J:423;
K:342;
K:403;
K:405;
K:411;
K:413;
K:415;
K:417;
K:419;
K:421;
K:423;
L:342;
L:405;
L:413;
L:415;
L:417;
L:419;
L:421;
L:423;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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Invalid;
Invalid;
Invalid;
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Invalid;
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Invalid;
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Invalid;
Invalid;
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Invalid;
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Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
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none;
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 submit data
78.133 C2 H6 O S CS(=O...
K A:343;
A:346;
B:343;
B:346;
C:342;
C:345;
D:344;
D:347;
E:343;
E:346;
F:345;
F:348;
G:344;
G:347;
H:342;
H:345;
I:342;
J:342;
J:345;
K:343;
K:346;
L:343;
L:346;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
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 submit data
39.098 K [K+]
NA A:344;
B:344;
C:343;
D:345;
E:344;
F:346;
G:345;
H:343;
I:343;
J:343;
K:344;
L:344;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
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 submit data
22.99 Na [Na+]
ZN A:345;
B:345;
C:344;
D:346;
E:345;
F:347;
G:346;
H:344;
I:344;
J:344;
K:345;
L:345;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
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 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ZUR 1.13 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF ACETYLPOLYAMINE AMIDOHYDROLASE FROM MYC RAMOSA IN COMPLEX WITH A HYDROXAMATE INHIBITOR MYCOPLANA RAMOSA ACETYLPOLYAMINE AMIDOHYDROLASE ARGINASE FOLD ENZYME-INHIBICOMPLEX POLYAMINE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: DESIGN, SYNTHESIS, AND EVALUATION OF POLYAMINE DEAC INHIBITORS, AND HIGH-RESOLUTION CRYSTAL STRUCTURES COMPLEXES WITH ACETYLPOLYAMINE AMIDOHYDROLASE. BIOCHEMISTRY V. 54 4692 2015
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 3Q9C - Q9C C9 H21 N3 O CC(=O)NCCC....
2 4ZUN ic50 = 26 uM SS9 C8 H20 N2 S C(CCNCCCN)....
3 4ZUM - FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
4 3Q9B - B3N C16 H25 N3 O3 CN(C)c1ccc....
5 4ZUQ ic50 = 0.13 uM 6XA C6 H14 N2 O2 C(CCC(=O)N....
6 4ZUP ic50 = 0.17 uM 5XA C5 H12 N2 O2 C(CCN)CC(=....
7 3Q9E - SP5 C12 H28 N4 O CC(=O)NCCC....
8 4ZUO ic50 = 0.39 uM XS6 C9 H21 N3 O2 C(CCC(=O)N....
9 4ZUR ic50 = 0.068 uM 7XA C7 H16 N2 O2 C(CCCN)CCC....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 3Q9C - Q9C C9 H21 N3 O CC(=O)NCCC....
2 4ZUN ic50 = 26 uM SS9 C8 H20 N2 S C(CCNCCCN)....
3 4ZUM - FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
4 3Q9B - B3N C16 H25 N3 O3 CN(C)c1ccc....
5 4ZUQ ic50 = 0.13 uM 6XA C6 H14 N2 O2 C(CCC(=O)N....
6 4ZUP ic50 = 0.17 uM 5XA C5 H12 N2 O2 C(CCN)CC(=....
7 3Q9E - SP5 C12 H28 N4 O CC(=O)NCCC....
8 4ZUO ic50 = 0.39 uM XS6 C9 H21 N3 O2 C(CCC(=O)N....
9 4ZUR ic50 = 0.068 uM 7XA C7 H16 N2 O2 C(CCCN)CCC....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 6PHT ic50 = 390 uM OKP C8 H21 B N2 O2 B(CCCCCNCC....
2 6PIC ic50 = 410 uM 6XA C6 H14 N2 O2 C(CCC(=O)N....
3 6PIA ic50 = 550 uM XS6 C9 H21 N3 O2 C(CCC(=O)N....
4 6PID ic50 = 380 uM OKS C8 H18 N2 O2 C(CCCC(=O)....
5 6PI1 ic50 = 160 uM B3N C16 H25 N3 O3 CN(C)c1ccc....
6 6PHZ ic50 = 350 uM FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
7 6PHR ic50 = 160 uM SS9 C8 H20 N2 S C(CCNCCCN)....
8 3Q9C - Q9C C9 H21 N3 O CC(=O)NCCC....
9 4ZUN ic50 = 26 uM SS9 C8 H20 N2 S C(CCNCCCN)....
10 4ZUM - FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
11 3Q9B - B3N C16 H25 N3 O3 CN(C)c1ccc....
12 4ZUQ ic50 = 0.13 uM 6XA C6 H14 N2 O2 C(CCC(=O)N....
13 4ZUP ic50 = 0.17 uM 5XA C5 H12 N2 O2 C(CCN)CC(=....
14 3Q9E - SP5 C12 H28 N4 O CC(=O)NCCC....
15 4ZUO ic50 = 0.39 uM XS6 C9 H21 N3 O2 C(CCC(=O)N....
16 4ZUR ic50 = 0.068 uM 7XA C7 H16 N2 O2 C(CCCN)CCC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: B3N; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 B3N 1 1
2 AH4 0.513889 0.738462
Similar Ligands (3D)
Ligand no: 1; Ligand: B3N; Similar ligands found: 6
No: Ligand Similarity coefficient
1 UFJ 0.9065
2 SHH 0.8989
3 EG2 0.8905
4 TSN 0.8870
5 2VZ 0.8602
6 BNI 0.8568
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4ZUR; Ligand: 7XA; 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: 4zur.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4ZUR; Ligand: 7XA; 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: 4zur.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
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