scPDB - 4z2t entry

Protein Data Bank Entry:

PDB ID : 4z2t

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2015-03-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-hydroxybiphenyl-3-monooxygenase
ID:	O06647_9PSED
AC:	O06647
Organism:	Pseudomonas nitroreducens
Reign:	Bacteria
TaxID:	46680
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.055
Number of residues:	63
Including
Standard Amino Acids:	57
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.592	1849.500

% Hydrophobic	% Polar
48.18	51.82
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	62.83 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
14.13	-32.3213	9.08606

Binding mode :

What is Poseview ?

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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
O2P	N	ALA- 17	3.14	157.19	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 46	3.85	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 46	3.2	126.44	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 46	3.36	166.34	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 46	2.64	131.71	H-Bond (Protein Donor)	false
O2'	NE	ARG- 46	2.76	129.57	H-Bond (Protein Donor)	false
C8M	CD	ARG- 46	4.33	0	Hydrophobic	false
C7	CG	ARG- 46	3.6	0	Hydrophobic	false
C8	CG	ARG- 46	3.84	0	Hydrophobic	false
C2'	CB	SER- 47	4.25	0	Hydrophobic	false
O2'	OE1	GLN- 120	2.97	152.2	H-Bond (Ligand Donor)	false
O4'	NE2	GLN- 120	3.23	132.8	H-Bond (Protein Donor)	false
N6A	O	TYR- 144	3.18	165.32	H-Bond (Ligand Donor)	false
N1A	N	TYR- 144	2.82	163.06	H-Bond (Protein Donor)	false
C1'	CZ2	TRP- 293	3.54	0	Hydrophobic	false
C7	CB	TRP- 293	4.11	0	Hydrophobic	false
DuAr	DuAr	TRP- 293	3.85	0	Aromatic Face/Face	false
O3'	OD1	ASP- 313	3.24	146.67	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 313	3.94	0	Hydrophobic	false
O1P	N	ASP- 313	2.73	146.96	H-Bond (Protein Donor)	false
O1P	O	HOH- 742	2.57	179.95	H-Bond (Protein Donor)	false
O2P	O	HOH- 776	2.72	157.6	H-Bond (Protein Donor)	false
O2	O	HOH- 784	2.87	149.79	H-Bond (Protein Donor)	false
O2A	O	HOH- 849	2.98	167.23	H-Bond (Protein Donor)	false