scPDB - 4yal entry

Protein Data Bank Entry:

PDB ID : 4yal

Resolution :1.880 Å

Experimental Method : X-ray

Deposition Date : 2015-02-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADPH--cytochrome P450 reductase
ID:	NCPR_RAT
AC:	P00388
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	86 %
B	14 %

Ligand binding site composition:

B-Factor:	25.458
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.074	1404.000

% Hydrophobic	% Polar
37.02	62.98
According to VolSite

Ligand :

HET Code:	2AM
Formula:	C10H12N5O7P
Molecular weight:	345.205 g/mol
DrugBank ID:	-
Buried Surface Area:	57.82 %
Polar Surface area:	201.54 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-8.81561	17.7261	33.8681

Binding mode :

What is Poseview ?

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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
C4'	CB	PRO- 533	4.17	0	Hydrophobic	false
C3'	CG	ARG- 567	4.49	0	Hydrophobic	false
O3P	OG	SER- 596	2.69	145.41	H-Bond (Protein Donor)	false
O2'	OG	SER- 596	2.87	133.56	H-Bond (Protein Donor)	false
O3'	OG	SER- 596	2.72	151.91	H-Bond (Ligand Donor)	false
C2'	CB	SER- 596	4.36	0	Hydrophobic	false
O2P	NH2	ARG- 597	3.07	153.14	H-Bond (Protein Donor)	false
O3P	NE	ARG- 597	2.87	177.99	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 597	3.89	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 597	3.7	0	Ionic (Protein Cationic)	false
O1P	NZ	LYS- 602	3.54	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 602	2.84	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 602	2.84	146.27	H-Bond (Protein Donor)	false
O1P	OH	TYR- 604	2.7	161.16	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 604	3.67	0	Aromatic Face/Face	false
C1'	CE1	TYR- 604	3.56	0	Hydrophobic	false
N1	NE2	GLN- 606	3.11	155.11	H-Bond (Protein Donor)	false
N6	OD2	ASP- 639	3.2	160.6	H-Bond (Ligand Donor)	false