scPDB - 4p0a entry

Protein Data Bank Entry:

PDB ID : 4p0a

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2014-02-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	E3 ubiquitin-protein ligase RNF31
ID:	RNF31_HUMAN
AC:	Q96EP0
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	6.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	81.814
Number of residues:	20
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.087	256.500

% Hydrophobic	% Polar
40.79	59.21
According to VolSite

Ligand :

HET Code:	ASP_LEU_TYR_GLY
Formula:	C21H29N4O8
Molecular weight:	465.477 g/mol
DrugBank ID:	-
Buried Surface Area:	40.13 %
Polar Surface area:	215.42 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
9.14803	-9.83518	-4.07182

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
CD2	CG2	ILE- 78	4.41	0	Hydrophobic	false
CD1	CB	LYS- 81	3.83	0	Hydrophobic	false
O	OH	TYR- 82	2.65	158.27	H-Bond (Protein Donor)	false
CB	CE1	TYR- 82	3.5	0	Hydrophobic	false
CD1	CZ	TYR- 82	4.27	0	Hydrophobic	false
CZ	CB	ASN- 85	4.31	0	Hydrophobic	false
OH	ND2	ASN- 85	3.12	151.47	H-Bond (Protein Donor)	false
CD1	CB	PRO- 92	4.36	0	Hydrophobic	false
CE1	CG	PRO- 92	3.91	0	Hydrophobic	false
CB	CB	TYR- 94	4.32	0	Hydrophobic	false
CD2	CG2	VAL- 98	4.38	0	Hydrophobic	false
O	ND2	ASN- 102	3.06	161.5	H-Bond (Protein Donor)	false
CD2	CG1	VAL- 104	3.64	0	Hydrophobic	false