scPDB - 2yjz entry

Protein Data Bank Entry:

PDB ID : 2yjz

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2011-05-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Metalloreductase STEAP4
ID:	STEA4_RAT
AC:	Q4V8K1
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	1.16.1

Chains:

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

Ligand binding site composition:

B-Factor:	40.760
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.357	303.750

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	59.75 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
49.2849	41.8944	45.1021

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
O3B	N	THR- 27	3.32	136.19	H-Bond (Protein Donor)	false
O2B	N	THR- 27	3.15	158.46	H-Bond (Protein Donor)	false
O1A	N	ASP- 29	3.23	160.65	H-Bond (Protein Donor)	false
O2N	N	PHE- 30	2.91	159.07	H-Bond (Protein Donor)	false
C5D	CB	PHE- 30	4.23	0	Hydrophobic	false
C3N	CB	PHE- 30	4.24	0	Hydrophobic	false
O2X	OG	SER- 49	2.63	159.51	H-Bond (Protein Donor)	false
O1X	N	ARG- 50	2.81	169.06	H-Bond (Protein Donor)	false
O1X	NE	ARG- 50	3.15	148.63	H-Bond (Protein Donor)	false
O3X	NE	ARG- 50	3.38	132.59	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 50	2.72	166.14	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 50	3.99	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 50	3.47	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 50	3.61	5.2	Pi/Cation	false
C1B	CG2	VAL- 81	3.87	0	Hydrophobic	false
DuAr	DuAr	HIS- 85	3.99	0	Aromatic Face/Face	false
C4D	CG2	VAL- 104	4.06	0	Hydrophobic	false
O2D	N	ASN- 106	3.02	176.11	H-Bond (Protein Donor)	false
O7N	N	ALA- 139	2.93	171.63	H-Bond (Protein Donor)	false
O2N	O	HOH- 2001	2.59	179.96	H-Bond (Protein Donor)	false
O4B	O	HOH- 2023	2.84	179.98	H-Bond (Protein Donor)	false