scPDB - 2jap entry

Protein Data Bank Entry:

PDB ID : 2jap

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Clavaldehyde dehydrogenase
ID:	Q9LCV7_STRCL
AC:	Q9LCV7
Organism:	Streptomyces clavuligerus
Reign:	Bacteria
TaxID:	1901
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.830
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.444	411.750

% Hydrophobic	% Polar
51.64	48.36
According to VolSite

Ligand :

HET Code:	J01
Formula:	C8H8NO5
Molecular weight:	198.153 g/mol
DrugBank ID:	DB00766
Buried Surface Area:	80.08 %
Polar Surface area:	89.9 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
29.0729	-18.0084	21.4684

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
C7	SD	MET- 95	3.66	0	Hydrophobic	false
C4	CB	ALA- 144	3.79	0	Hydrophobic	false
C4	CG2	VAL- 149	4.3	0	Hydrophobic	false
C4	CB	ALA- 152	3.52	0	Hydrophobic	false
C4	CD2	TYR- 155	3.88	0	Hydrophobic	false
C7	CE2	TYR- 155	4.07	0	Hydrophobic	false
O3	OH	TYR- 155	2.85	151.78	H-Bond (Protein Donor)	false
C4	CG	GLN- 156	4.39	0	Hydrophobic	false
O5	OG1	THR- 187	2.61	173.25	H-Bond (Protein Donor)	false
C7	CD2	LEU- 192	3.77	0	Hydrophobic	false
O5	OH	TYR- 205	2.7	164.8	H-Bond (Protein Donor)	false
O4	CZ	ARG- 208	3.86	0	Ionic (Protein Cationic)	false
C7	C3N	NDP- 1248	3.21	0	Hydrophobic	false