scPDB - 4dyd entry

Protein Data Bank Entry:

PDB ID : 4dyd

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2012-02-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diketoreductase
ID:	B1P3E1_ACIBI
AC:	B1P3E1
Organism:	Acinetobacter baylyi
Reign:	Bacteria
TaxID:	202950
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	46.566
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.274	259.875

% Hydrophobic	% Polar
63.64	36.36
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	54.83 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
39.3062	28.5488	70.604

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
O3B	N	THR- 12	2.76	158.54	H-Bond (Protein Donor)	false
O3B	OG1	THR- 12	3.48	126.04	H-Bond (Protein Donor)	false
C5N	CD2	LEU- 15	3.25	0	Hydrophobic	false
C3N	CD2	LEU- 15	3.21	0	Hydrophobic	false
O2B	OD1	ASP- 34	3.25	166.99	H-Bond (Ligand Donor)	false
C4D	CB	ALA- 92	4.38	0	Hydrophobic	false
C5B	CG	PRO- 94	3.9	0	Hydrophobic	false
C1B	CG	PRO- 94	4.27	0	Hydrophobic	false
C3D	CB	GLU- 95	4.35	0	Hydrophobic	false
O3D	OE1	GLU- 95	3	144.97	H-Bond (Ligand Donor)	false
O2D	OE1	GLU- 95	3.04	126.98	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 100	3.12	162.81	H-Bond (Protein Donor)	false
O4D	ND2	ASN- 120	2.88	130.5	H-Bond (Protein Donor)	false
O2D	N	SER- 122	2.97	151.31	H-Bond (Protein Donor)	false
O2D	OG	SER- 122	3.46	140.35	H-Bond (Protein Donor)	false
N1N	OG	SER- 122	3.47	145.3	H-Bond (Protein Donor)	false
C5N	CB	SER- 122	4.4	0	Hydrophobic	false