scPDB - 4nhy entry

Protein Data Bank Entry:

PDB ID : 4nhy

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2013-11-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prolyl 3-hydroxylase OGFOD1
ID:	OGFD1_HUMAN
AC:	Q8N543
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.14.11

Chains:

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

Ligand binding site composition:

B-Factor:	37.018
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.378	408.375

% Hydrophobic	% Polar
53.72	46.28
According to VolSite

Ligand :

HET Code:	PD2
Formula:	C7H3NO4
Molecular weight:	165.103 g/mol
DrugBank ID:	-
Buried Surface Area:	66.05 %
Polar Surface area:	93.15 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-10.2038	44.1611	-62.911

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
C3	CD2	LEU- 152	3.91	0	Hydrophobic	false
C4	CG1	ILE- 167	3.75	0	Hydrophobic	false
C5	CD1	LEU- 182	3.61	0	Hydrophobic	false
C4	CG2	VAL- 220	3.57	0	Hydrophobic	false
O42	NH1	ARG- 230	3.43	164.46	H-Bond (Protein Donor)	false
O41	NH2	ARG- 230	2.73	150.61	H-Bond (Protein Donor)	false
O41	NH1	ARG- 230	2.96	137.1	H-Bond (Protein Donor)	false
O41	CZ	ARG- 230	3.26	0	Ionic (Protein Cationic)	false
O42	OG	SER- 232	3.16	158.03	H-Bond (Protein Donor)	false
C3	CB	SER- 234	4.27	0	Hydrophobic	false
N1	MN	MN- 601	2.37	0	Metal Acceptor	false
O21	MN	MN- 601	2.11	0	Metal Acceptor	false
DuAr	MN	MN- 601	3.73	89.41	Pi/Cation	false