scPDB - 4u2l entry

Protein Data Bank Entry:

PDB ID : 4u2l

Resolution :1.340 Å

Experimental Method : X-ray

Deposition Date : 2014-07-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cholesterol oxidase
ID:	CHOD_STRS0
AC:	P12676
Organism:	Streptomyces sp.
Reign:	Bacteria
TaxID:	74576
EC Number:	1.1.3.6

Chains:

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

Ligand binding site composition:

B-Factor:	4.541
Number of residues:	71
Including
Standard Amino Acids:	68
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.175	1488.375

% Hydrophobic	% Polar
51.70	48.30
According to VolSite

Ligand :

HET Code:	SFD
Formula:	C27H33N9O18P2S
Molecular weight:	865.613 g/mol
DrugBank ID:	-
Buried Surface Area:	77.23 %
Polar Surface area:	439.77 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	8
Rings:	6
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
20.3472	0.69007	21.1093

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
C4R	CD1	TYR- 20	3.63	0	Hydrophobic	false
OP1	N	GLY- 21	3.19	165.36	H-Bond (Protein Donor)	false
O7R	OE1	GLU- 40	2.74	168.67	H-Bond (Ligand Donor)	false
O8R	OE2	GLU- 40	2.79	174.98	H-Bond (Ligand Donor)	false
N3A	N	MET- 41	3.16	141.6	H-Bond (Protein Donor)	false
C6R	CG	MET- 41	4.27	0	Hydrophobic	false
C3F	CD1	LEU- 96	4.21	0	Hydrophobic	false
C3F	CB	TYR- 107	4.13	0	Hydrophobic	false
OP3	N	GLY- 115	2.84	166.11	H-Bond (Protein Donor)	false
C3F	CG2	VAL- 118	3.74	0	Hydrophobic	false
C2R	CB	ASN- 119	4.5	0	Hydrophobic	false
C6F	CB	ASN- 119	3.29	0	Hydrophobic	false
O2R	ND2	ASN- 119	3.12	171.77	H-Bond (Protein Donor)	false
N3F	O	MET- 122	2.84	158.02	H-Bond (Ligand Donor)	false
O4F	N	MET- 122	2.9	156.75	H-Bond (Protein Donor)	false
CAF	CG1	ILE- 218	3.49	0	Hydrophobic	false
N1A	N	VAL- 250	3.06	156.05	H-Bond (Protein Donor)	false
N9	O	VAL- 250	3.01	162	H-Bond (Ligand Donor)	false
CAF	CD2	TYR- 446	4.26	0	Hydrophobic	false
C1F	CB	TYR- 446	4.08	0	Hydrophobic	false
O1	NE2	HIS- 447	3.3	132.18	H-Bond (Protein Donor)	false
O3	NE2	HIS- 447	2.95	160.69	H-Bond (Protein Donor)	false
OP2	N	GLY- 475	2.89	162.8	H-Bond (Protein Donor)	false
O3	ND2	ASN- 485	2.85	140.1	H-Bond (Protein Donor)	false
C1R	CG	PRO- 486	4.18	0	Hydrophobic	false
O2F	N	PHE- 487	2.76	171.96	H-Bond (Protein Donor)	false
C5R	CD1	ILE- 490	3.7	0	Hydrophobic	false
OP1	O	HOH- 890	2.72	164.7	H-Bond (Protein Donor)	false
O2F	O	HOH- 898	2.94	127.37	H-Bond (Protein Donor)	false