scPDB - 2eix entry

Protein Data Bank Entry:

PDB ID : 2eix

Resolution :1.560 Å

Experimental Method : X-ray

Deposition Date : 2007-03-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADH-cytochrome b5 reductase
ID:	Q1HA49_PHYPO
AC:	Q1HA49
Organism:	Physarum polycephalum
Reign:	Eukaryota
TaxID:	5791
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	24 %
B	76 %

Ligand binding site composition:

B-Factor:	14.805
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.373	2139.750

% Hydrophobic	% Polar
46.85	53.15
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	65.78 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-4.13258	-21.243	-16.2256

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
C7M	CB	HIS- 85	4.16	0	Hydrophobic	false
O1A	NH1	ARG- 99	3.44	120.69	H-Bond (Protein Donor)	false
O1P	NE	ARG- 99	2.78	149.49	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 99	2.92	140.12	H-Bond (Protein Donor)	false
C2'	CB	ARG- 99	4.34	0	Hydrophobic	false
C3'	CD	ARG- 99	4.02	0	Hydrophobic	false
O1P	CZ	ARG- 99	3.32	0	Ionic (Protein Cationic)	false
O2'	O	PRO- 100	2.7	177.4	H-Bond (Ligand Donor)	false
C7	CB	PRO- 100	4.09	0	Hydrophobic	false
C8M	CG	PRO- 100	3.41	0	Hydrophobic	false
C8	CG	PRO- 100	3.51	0	Hydrophobic	false
C3'	CZ	TYR- 101	4.5	0	Hydrophobic	false
C4'	CE1	TYR- 101	4.45	0	Hydrophobic	false
C2'	CE1	TYR- 101	3.78	0	Hydrophobic	false
O4'	OH	TYR- 101	2.73	140.92	H-Bond (Protein Donor)	false
N5	N	THR- 102	3.3	136.86	H-Bond (Protein Donor)	false
C6	CB	THR- 102	4.3	0	Hydrophobic	false
N3	O	ILE- 116	2.71	171.49	H-Bond (Ligand Donor)	false
O2	N	LYS- 118	3.04	152.58	H-Bond (Protein Donor)	false
C5B	CG	TYR- 120	3.95	0	Hydrophobic	false
C4B	CD1	TYR- 120	4.32	0	Hydrophobic	false
C3B	CB	TYR- 120	4.35	0	Hydrophobic	false
C5'	CE2	TYR- 120	3.84	0	Hydrophobic	false
O3B	N	LYS- 122	3.44	148.93	H-Bond (Protein Donor)	false
C3B	CB	LYS- 122	4.17	0	Hydrophobic	false
O1P	N	MET- 125	2.86	160.09	H-Bond (Protein Donor)	false
O2P	OG	SER- 126	2.78	149.23	H-Bond (Protein Donor)	false
O2P	N	SER- 126	2.82	158.75	H-Bond (Protein Donor)	false
C6	CG	PRO- 168	3.73	0	Hydrophobic	false
C2B	CE2	PHE- 233	3.89	0	Hydrophobic	false
C1B	CZ	PHE- 233	4.23	0	Hydrophobic	false
DuAr	DuAr	PHE- 233	3.77	0	Aromatic Face/Face	false
N6A	O	VAL- 234	2.98	131.77	H-Bond (Ligand Donor)	false
C8	SG	CYS- 255	4.14	0	Hydrophobic	false
C5B	CE	MET- 259	4.25	0	Hydrophobic	false
C1B	CG	MET- 259	3.91	0	Hydrophobic	false
O3'	NZ	LYS- 262	3.34	122.7	H-Bond (Protein Donor)	false
C7M	CB	PHE- 281	4.08	0	Hydrophobic	false
O1A	O	HOH- 1654	2.6	179.95	H-Bond (Protein Donor)	false