scPDB - 4bur entry

Protein Data Bank Entry:

PDB ID : 4bur

Resolution :2.880 Å

Experimental Method : X-ray

Deposition Date : 2013-06-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Apoptosis-inducing factor 1, mitochondrial
ID:	AIFM1_HUMAN
AC:	O95831
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	37.412
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.798	1134.000

% Hydrophobic	% Polar
41.67	58.33
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	63.21 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
53.7808	-32.9512	-64.824

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
O2B	N	GLY- 308	2.95	158.96	H-Bond (Protein Donor)	false
O2A	N	PHE- 310	3.11	158.48	H-Bond (Protein Donor)	false
C2D	CD2	PHE- 310	3.88	0	Hydrophobic	false
C3N	CB	PHE- 310	3.33	0	Hydrophobic	false
O2N	N	LEU- 311	2.89	157.56	H-Bond (Protein Donor)	false
C5D	CB	LEU- 311	4.49	0	Hydrophobic	false
C5N	CB	LEU- 311	4.03	0	Hydrophobic	false
N7N	OE2	GLU- 314	3.18	132.17	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 336	2.83	162.37	H-Bond (Ligand Donor)	false
C5B	CD	LYS- 342	4.41	0	Hydrophobic	false
C3B	CD	LYS- 342	3.77	0	Hydrophobic	false
C1B	CB	VAL- 398	4.2	0	Hydrophobic	false
O1N	N	GLY- 399	2.82	158	H-Bond (Protein Donor)	false
C3D	CG	LEU- 400	4.41	0	Hydrophobic	false
C4D	CD2	LEU- 400	3.86	0	Hydrophobic	false
O3D	OE1	GLU- 453	2.81	173.63	H-Bond (Ligand Donor)	false
O2D	O	GLU- 453	3.05	143.41	H-Bond (Ligand Donor)	false
N7N	O	TRP- 483	3.12	154.24	H-Bond (Ligand Donor)	false
O2N	O	HOH- 2006	2.79	179.96	H-Bond (Protein Donor)	false