scPDB - 1rp4 entry

Protein Data Bank Entry:

PDB ID : 1rp4

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2003-12-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Endoplasmic oxidoreductin-1
ID:	ERO1_YEAST
AC:	Q03103
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.8.4

Chains:

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

Ligand binding site composition:

B-Factor:	43.536
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.105	435.375

% Hydrophobic	% Polar
59.69	40.31
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	58.27 %
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
36.2894	53.2386	16.8423

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
C5'	CG1	VAL- 107	3.57	0	Hydrophobic	false
N3	O	ARG- 187	2.85	169.76	H-Bond (Ligand Donor)	false
O2	N	THR- 189	2.92	168.95	H-Bond (Protein Donor)	false
C8M	CE2	TYR- 191	4.47	0	Hydrophobic	false
C1'	CD2	TYR- 191	3.76	0	Hydrophobic	false
C8M	CG2	ILE- 199	3.57	0	Hydrophobic	false
C7M	CH2	TRP- 200	4.11	0	Hydrophobic	false
C8M	CE2	TRP- 200	3.43	0	Hydrophobic	false
O2'	NE1	TRP- 200	2.97	152.76	H-Bond (Protein Donor)	false
O3'	NE1	TRP- 200	3.42	129.58	H-Bond (Protein Donor)	false
N6A	O	SER- 228	2.87	136.31	H-Bond (Ligand Donor)	false
N1A	OG	SER- 228	2.71	170.48	H-Bond (Protein Donor)	false
C7M	CZ	PHE- 230	3.98	0	Hydrophobic	false
O1A	NE2	HIS- 231	2.76	156.35	H-Bond (Protein Donor)	false
C9A	CG2	ILE- 234	4.47	0	Hydrophobic	false
C6	CD1	ILE- 234	3.61	0	Hydrophobic	false
C2'	CD2	LEU- 238	4.11	0	Hydrophobic	false
O4'	NH1	ARG- 260	2.91	138.5	H-Bond (Protein Donor)	false
O4'	NH2	ARG- 260	3.05	133.57	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 260	3.58	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 267	3.11	125.85	H-Bond (Protein Donor)	false
C7M	SD	MET- 347	3.29	0	Hydrophobic	false
C7M	CG2	VAL- 350	4.34	0	Hydrophobic	false
C6	CB	CYS- 355	4.08	0	Hydrophobic	false
C9A	CB	CYS- 355	4.45	0	Hydrophobic	false