scPDB - 2vdm entry

Protein Data Bank Entry:

PDB ID : 2vdm

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2007-10-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Integrin alpha-IIb	Integrin beta-3
ID:	ITA2B_HUMAN	ITB3_HUMAN
AC:	P08514	P05106
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	43 %
B	57 %

Ligand binding site composition:

B-Factor:	50.209
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG CA

Cavity properties

Ligandability	Volume (Å3)
0.755	499.500

% Hydrophobic	% Polar
50.68	49.32
According to VolSite

Ligand :

HET Code:	AGG
Formula:	C22H36N2O5S
Molecular weight:	440.597 g/mol
DrugBank ID:	DB00775
Buried Surface Area:	58.39 %
Polar Surface area:	120.52 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
94.7309	36.0998	78.8366

Binding mode :

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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
CA	CB	TYR- 122	4.35	0	Hydrophobic	false
O	N	TYR- 122	3.14	140.31	H-Bond (Protein Donor)	false
CA	CB	SER- 123	4.38	0	Hydrophobic	false
CD2	CB	SER- 123	4.47	0	Hydrophobic	false
OXT	N	SER- 123	2.7	152.12	H-Bond (Protein Donor)	false
C3	CZ	PHE- 160	4.37	0	Hydrophobic	false
C2	CE1	PHE- 160	3.55	0	Hydrophobic	false
C11	CE1	TYR- 190	4.19	0	Hydrophobic	false
C13	CG	TYR- 190	4.39	0	Hydrophobic	false
C15	CB	TYR- 190	3.91	0	Hydrophobic	false
C16	CD1	LEU- 192	3.32	0	Hydrophobic	false
O1	NE	ARG- 214	3.08	126.5	H-Bond (Protein Donor)	false
N	O	ASN- 215	2.76	145.88	H-Bond (Ligand Donor)	false
O	ND2	ASN- 215	2.55	128.14	H-Bond (Protein Donor)	false
O	N	ASN- 215	3.11	151.17	H-Bond (Protein Donor)	false
CE1	CB	ALA- 218	3.99	0	Hydrophobic	false
N18	OD2	ASP- 224	3.55	0	Ionic (Ligand Cationic)	false
N18	OD1	ASP- 224	3.05	0	Ionic (Ligand Cationic)	false
N18	OD1	ASP- 224	3.05	131.8	H-Bond (Ligand Donor)	false
C14	CZ	PHE- 231	4.29	0	Hydrophobic	false
C16	CE2	PHE- 231	3.82	0	Hydrophobic	false
OXT	MG	MG- 2001	2.36	0	Metal Acceptor	false