scPDB - 2wpx entry

Protein Data Bank Entry:

PDB ID : 2wpx

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 2009-08-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Orf14
ID:	Q8KRB5_STRCL
AC:	Q8KRB5
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:	18.183
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.156	1481.625

% Hydrophobic	% Polar
51.71	48.29
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	51.73 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-85.9375	100.714	42.6172

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
CEP	CD2	LEU- 90	3.99	0	Hydrophobic	false
N4P	O	LEU- 90	2.9	155.45	H-Bond (Ligand Donor)	false
CCP	CG2	VAL- 92	3.69	0	Hydrophobic	false
O9P	N	VAL- 92	2.93	151.12	H-Bond (Protein Donor)	false
CCP	CG	ARG- 97	4.25	0	Hydrophobic	false
CAP	CD	ARG- 97	3.71	0	Hydrophobic	false
C3B	CD	ARG- 98	4.43	0	Hydrophobic	false
C5B	CD	ARG- 98	4.4	0	Hydrophobic	false
O8A	CZ	ARG- 98	3.54	0	Ionic (Protein Cationic)	false
O4A	N	ARG- 98	2.72	163.96	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 98	3.72	164.97	Pi/Cation	false
O2A	N	GLY- 100	2.8	141.79	H-Bond (Protein Donor)	false
O5A	N	GLY- 102	2.81	150.31	H-Bond (Protein Donor)	false
CH3	CZ3	TRP- 106	3.87	0	Hydrophobic	false
CH3	CB	ALA- 123	3.64	0	Hydrophobic	false
S1P	CG2	VAL- 125	4.09	0	Hydrophobic	false
CH3	CG2	VAL- 125	4.45	0	Hydrophobic	false
S1P	CB	PRO- 139	4.35	0	Hydrophobic	false
C4B	CD1	PHE- 142	4.27	0	Hydrophobic	false
CEP	CD2	PHE- 142	3.72	0	Hydrophobic	false
CDP	CG	PHE- 142	3.58	0	Hydrophobic	false
C2P	CD2	PHE- 142	3.54	0	Hydrophobic	false
S1P	CB	ALA- 143	4.32	0	Hydrophobic	false
CH3	CB	ALA- 143	3.79	0	Hydrophobic	false
C4B	CB	ALA- 145	4.33	0	Hydrophobic	false
C1B	CB	ALA- 145	4.13	0	Hydrophobic	false
O5A	O	HOH- 2101	3.11	165.25	H-Bond (Protein Donor)	false