scPDB - 4pzd entry

Protein Data Bank Entry:

PDB ID : 4pzd

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2014-03-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-Hydroxyacyl-CoA dehydrogenase
ID:	Q0KEY8_CUPNH
AC:	Q0KEY8
Organism:	Cupriavidus necator
Reign:	Bacteria
TaxID:	381666
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	56.207
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.221	725.625

% Hydrophobic	% Polar
51.63	48.37
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	53.96 %
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
-33.7842	-131.024	49.9262

Binding mode :

What is Poseview ?

2D View
3D View

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
O2A	N	THR- 13	3.2	158.67	H-Bond (Protein Donor)	false
O2N	N	MET- 14	2.77	161.15	H-Bond (Protein Donor)	false
C5D	CB	MET- 14	4.18	0	Hydrophobic	false
C4D	CG	MET- 14	4.34	0	Hydrophobic	false
C3N	CG	MET- 14	4.18	0	Hydrophobic	false
C5N	SD	MET- 14	3.93	0	Hydrophobic	false
O3B	OD1	ASP- 33	3.47	133.38	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 33	2.98	165.04	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 33	2.78	166.19	H-Bond (Ligand Donor)	false
N6A	OH	TYR- 77	3.23	120.08	H-Bond (Ligand Donor)	false
N1A	OH	TYR- 77	2.76	170.87	H-Bond (Protein Donor)	false
O2D	OE2	GLU- 92	3.24	120.66	H-Bond (Ligand Donor)	false
C2D	CG	GLU- 92	3.8	0	Hydrophobic	false
O2D	O	ASN- 117	3.28	120.58	H-Bond (Ligand Donor)	false
N1N	ND2	ASN- 117	3.35	139.32	H-Bond (Protein Donor)	false
C5N	CB	SER- 119	4.01	0	Hydrophobic	false