scPDB - 3vgw entry

Protein Data Bank Entry:

PDB ID : 3vgw

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2011-08-21

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
E	97 %
G	3 %

Ligand binding site composition:

B-Factor:	16.438
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.704	432.000

% Hydrophobic	% Polar
47.66	52.34
According to VolSite

Ligand :

HET Code:	NVZ
Formula:	C12H17N2O4S
Molecular weight:	285.339 g/mol
DrugBank ID:	-
Buried Surface Area:	87.67 %
Polar Surface area:	114.84 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
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
95.9303	35.1021	65.9243

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
O3	ND2	ASN- 12	3.14	154.07	H-Bond (Protein Donor)	false
C18	CD2	LEU- 14	3.43	0	Hydrophobic	false
O3	OG	SER- 16	2.69	153.98	H-Bond (Protein Donor)	false
O3	OH	TYR- 33	2.7	173.7	H-Bond (Protein Donor)	false
N2	OG1	THR- 35	2.83	158.6	H-Bond (Ligand Donor)	false
C7	CB	THR- 35	4.33	0	Hydrophobic	false
C9	CG2	THR- 35	4.41	0	Hydrophobic	false
C9	CB	THR- 38	4.47	0	Hydrophobic	false
O12	N	ALA- 39	2.79	156.03	H-Bond (Protein Donor)	false
O12	N	THR- 40	3.12	168.2	H-Bond (Protein Donor)	false
C9	CE2	TRP- 70	3.69	0	Hydrophobic	false
C10	CD2	TRP- 70	3.75	0	Hydrophobic	false
S1	CZ2	TRP- 70	3.71	0	Hydrophobic	false
C8	CZ2	TRP- 70	3.56	0	Hydrophobic	false
C9	CZ	PHE- 72	3.64	0	Hydrophobic	false
O11	OG	SER- 73	3.03	170.78	H-Bond (Protein Donor)	false
S1	CG2	THR- 77	3.8	0	Hydrophobic	false
S1	CZ	PHE- 79	4.21	0	Hydrophobic	false
C6	CE2	TRP- 97	3.61	0	Hydrophobic	false
C2	CD2	LEU- 99	4.32	0	Hydrophobic	false
C8	CD2	LEU- 99	4.04	0	Hydrophobic	false
C2	CZ3	TRP- 110	3.54	0	Hydrophobic	false
C6	CZ3	TRP- 110	4.04	0	Hydrophobic	false
C7	CH2	TRP- 110	4.25	0	Hydrophobic	false