scPDB - 2b4d entry

Protein Data Bank Entry:

PDB ID : 2b4d

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2005-09-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diamine acetyltransferase 1
ID:	SAT1_HUMAN
AC:	P21673
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	25.132
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.912	1461.375

% Hydrophobic	% Polar
43.19	56.81
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	43.99 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
18.8329	15.3685	21.3625

Binding mode :

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CEP	CE2	PHE- 94	3.34	0	Hydrophobic	false
O1A	N	GLY- 102	3.06	120.88	H-Bond (Protein Donor)	false
O4A	N	GLY- 102	2.97	146.17	H-Bond (Protein Donor)	false
O1A	N	GLY- 104	2.89	153.54	H-Bond (Protein Donor)	false
O3A	N	GLY- 106	3.45	124.45	H-Bond (Protein Donor)	false
O5A	N	GLY- 106	2.79	148.01	H-Bond (Protein Donor)	false
O2A	N	SER- 107	2.94	143.79	H-Bond (Protein Donor)	false
S1P	CD1	PHE- 127	4.12	0	Hydrophobic	false
S1P	CB	VAL- 129	3.86	0	Hydrophobic	false
C2P	CB	SER- 136	4.22	0	Hydrophobic	false
CDP	CE2	PHE- 139	3.69	0	Hydrophobic	false
CEP	CZ	PHE- 139	4.41	0	Hydrophobic	false
C4B	CE2	PHE- 139	4.02	0	Hydrophobic	false
S1P	CE2	TYR- 140	3.55	0	Hydrophobic	false
O8A	NH1	ARG- 142	3.03	160.5	H-Bond (Protein Donor)	false
O9A	CZ	ARG- 142	3.48	0	Ionic (Protein Cationic)	false
O7A	NH2	ARG- 143	2.51	149.85	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 143	3.14	132.35	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 143	3.52	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 143	3.73	0	Ionic (Protein Cationic)	false
O5A	O	HOH- 231	3.07	179.98	H-Bond (Protein Donor)	false