scPDB - 3vhh entry

Protein Data Bank Entry:

PDB ID : 3vhh

Resolution :2.260 Å

Experimental Method : X-ray

Deposition Date : 2011-08-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Avidin
ID:	AVID_CHICK
AC:	P02701
Organism:	Gallus gallus
Reign:	Eukaryota
TaxID:	9031
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	97 %
D	3 %

Ligand binding site composition:

B-Factor:	21.796
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.815	354.375

% Hydrophobic	% Polar
46.67	53.33
According to VolSite

Ligand :

HET Code:	VHH
Formula:	C12H19N2O3S
Molecular weight:	271.356 g/mol
DrugBank ID:	-
Buried Surface Area:	85.58 %
Polar Surface area:	88.98 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
20.0138	4.14133	28.6149

Binding mode :

What is Poseview ?

2D View
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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
O3	ND2	ASN- 12	3.38	172.93	H-Bond (Protein Donor)	false
O3	OG	SER- 16	2.81	166.1	H-Bond (Protein Donor)	false
O3	OH	TYR- 33	2.63	166.75	H-Bond (Protein Donor)	false
C9	CB	THR- 38	4.2	0	Hydrophobic	false
O11	N	ALA- 39	2.85	147.41	H-Bond (Protein Donor)	false
C9	CE2	TRP- 70	3.7	0	Hydrophobic	false
S1	CZ2	TRP- 70	3.75	0	Hydrophobic	false
C9	CZ	PHE- 72	3.68	0	Hydrophobic	false
O12	OG	SER- 73	2.72	161.79	H-Bond (Protein Donor)	false
O12	OG	SER- 75	3.38	142.71	H-Bond (Protein Donor)	false
S1	CG2	THR- 77	3.89	0	Hydrophobic	false
C6	CZ	PHE- 79	4.4	0	Hydrophobic	false
C6	CD2	TRP- 97	3.51	0	Hydrophobic	false
C2	CD2	LEU- 99	4.26	0	Hydrophobic	false
C2	CZ3	TRP- 110	3.41	0	Hydrophobic	false
C6	CZ3	TRP- 110	4.41	0	Hydrophobic	false