scPDB - 2pv7 entry

Protein Data Bank Entry:

PDB ID : 2pv7

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-05-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	T-protein
ID:	TYRA_HAEIN
AC:	P43902
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	1.3.1.12

Chains:

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

Ligand binding site composition:

B-Factor:	32.741
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.109	664.875

% Hydrophobic	% Polar
51.27	48.73
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.33 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
27.3055	76.5297	35.3674

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
O1A	N	LYS- 111	3.08	168.19	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 111	2.76	173.17	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 111	2.76	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 111	4	0	Ionic (Protein Cationic)	false
O1N	N	LEU- 112	2.71	172.71	H-Bond (Protein Donor)	false
C5N	CD2	LEU- 112	3.69	0	Hydrophobic	false
O3B	OD1	ASP- 131	3.32	125.55	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 131	2.87	161.85	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 131	2.59	153.61	H-Bond (Ligand Donor)	false
N1A	NE1	TRP- 135	3.02	177.02	H-Bond (Protein Donor)	false
O3D	O	VAL- 152	2.88	131.61	H-Bond (Ligand Donor)	false
C5B	CG	PRO- 153	4.35	0	Hydrophobic	false
C3D	CG1	ILE- 154	4.04	0	Hydrophobic	false
O2D	OG	SER- 179	2.64	154.7	H-Bond (Ligand Donor)	false
O2D	N	SER- 179	2.86	141.83	H-Bond (Protein Donor)	false
C2D	CD1	LEU- 305	3.65	0	Hydrophobic	false
C3N	CD2	LEU- 305	4.12	0	Hydrophobic	false
O3D	O	HOH- 406	2.99	134.76	H-Bond (Ligand Donor)	false
O1N	O	HOH- 413	2.93	179.95	H-Bond (Protein Donor)	false
N6A	O	HOH- 436	2.93	127.02	H-Bond (Ligand Donor)	false