scPDB - 4nhk entry

Protein Data Bank Entry:

PDB ID : 4nhk

Resolution :1.900 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 3,4-dihydroxylase TPA1
ID:	TPA1_YEAST
AC:	P40032
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.14.11

Chains:

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

Ligand binding site composition:

B-Factor:	32.976
Number of residues:	24
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.571	533.250

% Hydrophobic	% Polar
46.20	53.80
According to VolSite

Ligand :

HET Code:	PD2
Formula:	C7H3NO4
Molecular weight:	165.103 g/mol
DrugBank ID:	-
Buried Surface Area:	65.62 %
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
337.375	36.3313	155.725

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
C3	CD2	LEU- 156	3.76	0	Hydrophobic	false
C5	CG1	ILE- 171	3.86	0	Hydrophobic	false
C5	CG2	VAL- 229	3.43	0	Hydrophobic	false
O42	OG	SER- 240	3.18	131.49	H-Bond (Protein Donor)	false
O41	OG	SER- 240	3.02	162.34	H-Bond (Protein Donor)	false
C4	CB	GLN- 242	4.26	0	Hydrophobic	false
C3	CG	GLN- 242	3.88	0	Hydrophobic	false
N1	MN	MN- 701	2.28	0	Metal Acceptor	false
O22	MN	MN- 701	2.1	0	Metal Acceptor	false
DuAr	MN	MN- 701	3.63	82.56	Pi/Cation	false