scPDB - 5a9s entry

Protein Data Bank Entry:

PDB ID : 5a9s

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2015-07-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative dehydrogenase
ID:	R4SNK4_AMYOR
AC:	R4SNK4
Organism:	Amycolatopsis orientalis HCCB10007
Reign:	Bacteria
TaxID:	1156913
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	84 %
B	16 %

Ligand binding site composition:

B-Factor:	37.412
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.171	637.875

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	53.49 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
32.0078	0.313958	-31.3096

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	N	LEU- 13	3.06	129.68	H-Bond (Protein Donor)	false
O3B	N	GLY- 14	3.14	124.47	H-Bond (Protein Donor)	false
O1N	N	MET- 16	2.88	150.1	H-Bond (Protein Donor)	false
O2N	N	MET- 16	3.36	131.81	H-Bond (Protein Donor)	false
C5D	CB	MET- 16	3.88	0	Hydrophobic	false
C3N	CE	MET- 16	3.26	0	Hydrophobic	false
O3X	ND2	ASN- 35	3.04	161.2	H-Bond (Protein Donor)	false
O1X	NE	ARG- 36	3.31	159.09	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 36	2.63	153.1	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 36	3.94	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 36	3.7	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 36	3.86	157.08	Pi/Cation	false
O1X	N	SER- 37	2.64	150.56	H-Bond (Protein Donor)	false
O1X	OG	SER- 37	2.56	150.87	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 40	2.72	161.01	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 40	2.72	0	Ionic (Protein Cationic)	false
C5D	SG	CYS- 68	3.24	0	Hydrophobic	false
C1B	CD2	LEU- 69	4.16	0	Hydrophobic	false
C1B	CB	ALA- 70	4.03	0	Hydrophobic	false
C5B	CB	ALA- 70	3.71	0	Hydrophobic	false
C4D	CB	ASN- 95	3.8	0	Hydrophobic	false
O2D	OD1	ASN- 95	2.6	167.39	H-Bond (Ligand Donor)	false
C5N	CB	ILE- 121	4.01	0	Hydrophobic	false