scPDB - 5b1y entry

Protein Data Bank Entry:

PDB ID : 5b1y

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2015-12-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-oxoacyl-[acyl-carrier-protein] reductase
ID:	Q9Y8Y1_AERPE
AC:	Q9Y8Y1
Organism:	Aeropyrum pernix
Reign:	Archaea
TaxID:	272557
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.061
Number of residues:	51
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.166	678.375

% Hydrophobic	% Polar
46.27	53.73
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	71.73 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-20.4738	13.6916	23.5004

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
O3B	O	GLY- 10	3.41	120.66	H-Bond (Ligand Donor)	false
N3A	N	GLY- 10	3.39	122.56	H-Bond (Protein Donor)	false
C3B	CB	ARG- 13	4.31	0	Hydrophobic	false
O2N	N	ILE- 15	3.12	145.67	H-Bond (Protein Donor)	false
O1X	N	LYS- 35	2.67	121.37	H-Bond (Protein Donor)	false
O1X	N	SER- 36	2.99	131.92	H-Bond (Protein Donor)	false
O2X	N	ARG- 37	3.22	156.22	H-Bond (Protein Donor)	false
C4D	CB	ALA- 89	4.29	0	Hydrophobic	false
C1B	CB	ALA- 90	4.19	0	Hydrophobic	false
O3D	N	GLY- 91	3.14	131.42	H-Bond (Protein Donor)	false
C4D	CG1	VAL- 139	3.79	0	Hydrophobic	false
C5N	CB	SER- 141	3.57	0	Hydrophobic	false
O2D	OH	TYR- 155	2.97	148.22	H-Bond (Protein Donor)	false
C2D	CE	LYS- 159	4.23	0	Hydrophobic	false
C4N	CB	PRO- 185	4.22	0	Hydrophobic	false
C5N	CG	PRO- 185	3.65	0	Hydrophobic	false
O7N	N	VAL- 188	2.84	148.98	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 188	4.29	0	Hydrophobic	false
O2N	O	HOH- 450	2.97	179.98	H-Bond (Protein Donor)	false