scPDB - 1rd4 entry

Protein Data Bank Entry:

PDB ID : 1rd4

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2003-11-05

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	100 %

Ligand binding site composition:

B-Factor:	11.563
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.431	712.125

% Hydrophobic	% Polar
59.72	40.28
According to VolSite

Ligand :

HET Code:	L08
Formula:	C25H26N4O4S
Molecular weight:	478.563 g/mol
DrugBank ID:	DB02177
Buried Surface Area:	58.11 %
Polar Surface area:	116.79 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
0.968588	-8.33812	-7.01874

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
C8	CD1	LEU- 132	3.95	0	Hydrophobic	false
N20	OH	TYR- 166	2.92	172.21	H-Bond (Protein Donor)	false
C19	CG2	VAL- 233	3.32	0	Hydrophobic	false
C12	CD1	ILE- 235	3.45	0	Hydrophobic	false
C19	CD1	ILE- 255	3.94	0	Hydrophobic	false
C19	CE1	TYR- 257	4.47	0	Hydrophobic	false
C6	CB	TYR- 257	3.6	0	Hydrophobic	false
S1	CD1	ILE- 259	3.62	0	Hydrophobic	false
C6	CG1	ILE- 259	3.58	0	Hydrophobic	false
C6	CB	LYS- 287	4.06	0	Hydrophobic	false
C3	CG	LYS- 287	3.62	0	Hydrophobic	false
C4	CB	LYS- 287	3.69	0	Hydrophobic	false
S1	CD2	LEU- 298	3.73	0	Hydrophobic	false
C2	CD1	LEU- 298	4.03	0	Hydrophobic	false
C9	CD1	LEU- 298	4.3	0	Hydrophobic	false
C33	CG	GLU- 301	4.26	0	Hydrophobic	false
C10	CG	LEU- 302	4.2	0	Hydrophobic	false
C12	CD1	LEU- 302	4.13	0	Hydrophobic	false
C33	CG	LEU- 302	4.02	0	Hydrophobic	false
C14	CD2	LEU- 302	4.2	0	Hydrophobic	false
C33	CD	LYS- 305	4.02	0	Hydrophobic	false