scPDB - 1xdd entry

Protein Data Bank Entry:

PDB ID : 1xdd

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2004-09-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Integrin alpha-L
ID:	ITAL_HUMAN
AC:	P20701
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	74 %
B	26 %

Ligand binding site composition:

B-Factor:	34.548
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.399	1009.125

% Hydrophobic	% Polar
58.19	41.81
According to VolSite

Ligand :

HET Code:	AAY
Formula:	C37H49NO6
Molecular weight:	603.788 g/mol
DrugBank ID:	DB03932
Buried Surface Area:	60.35 %
Polar Surface area:	96.3 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.4963	89.3733	42.9461

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
C85	CA	GLY- 128	3.94	0	Hydrophobic	false
C85	CG2	VAL- 130	4.11	0	Hydrophobic	false
C90	CG2	VAL- 130	3.68	0	Hydrophobic	false
C42	CD1	LEU- 132	3.53	0	Hydrophobic	false
C46	CZ	PHE- 153	4.04	0	Hydrophobic	false
C42	CE2	TYR- 166	3.98	0	Hydrophobic	false
C78	CG2	THR- 231	3.93	0	Hydrophobic	false
C72	CG2	THR- 231	4.01	0	Hydrophobic	false
C42	CG1	VAL- 233	4.04	0	Hydrophobic	false
C69	CG2	VAL- 233	4.43	0	Hydrophobic	false
C24	CD1	ILE- 235	3.74	0	Hydrophobic	false
C31	CD1	ILE- 235	3.8	0	Hydrophobic	false
C78	CD1	ILE- 255	4.32	0	Hydrophobic	false
C70	CD1	ILE- 255	3.95	0	Hydrophobic	false
C26	CZ	TYR- 257	3.76	0	Hydrophobic	false
C28	CD2	TYR- 257	3.71	0	Hydrophobic	false
C24	CE1	TYR- 257	4.21	0	Hydrophobic	false
C19	CE1	TYR- 257	3.95	0	Hydrophobic	false
C9	CZ	TYR- 257	4.42	0	Hydrophobic	false
C31	CD1	ILE- 259	4.49	0	Hydrophobic	false
C46	CG	LEU- 298	3.98	0	Hydrophobic	false
C62	CG	GLU- 301	3.88	0	Hydrophobic	false
C53	CD1	LEU- 302	4.1	0	Hydrophobic	false
C58	CD1	LEU- 302	4.34	0	Hydrophobic	false
C22	CD1	LEU- 302	4.28	0	Hydrophobic	false
C81	CB	GLN- 303	4.42	0	Hydrophobic	false
C78	CD	LYS- 304	3.73	0	Hydrophobic	false
C7	CD	LYS- 304	3.97	0	Hydrophobic	false
C70	CD	LYS- 304	3.75	0	Hydrophobic	false
C90	CB	LYS- 304	4.26	0	Hydrophobic	false
C72	CG	LYS- 304	3.64	0	Hydrophobic	false
C55	CB	LYS- 305	3.92	0	Hydrophobic	false
C58	CD1	ILE- 306	3.7	0	Hydrophobic	false
C16	CD1	ILE- 306	4.37	0	Hydrophobic	false
O52	O	HOH- 433	2.69	179.98	H-Bond (Protein Donor)	false