scPDB - 4nhm entry

Protein Data Bank Entry:

PDB ID : 4nhm

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:	30.589
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.224	425.250

% Hydrophobic	% Polar
45.24	54.76
According to VolSite

Ligand :

HET Code:	UN9
Formula:	C12H8ClN2O4
Molecular weight:	279.656 g/mol
DrugBank ID:	DB08687
Buried Surface Area:	66.17 %
Polar Surface area:	102.35 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
169.261	40.6764	156.539

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
O19	OH	TYR- 150	2.81	157.99	H-Bond (Protein Donor)	false
C10	CD2	LEU- 156	3.46	0	Hydrophobic	false
O17	OH	TYR- 173	2.64	172.84	H-Bond (Protein Donor)	false
O18	NH1	ARG- 238	2.73	163.03	H-Bond (Protein Donor)	false
O17	NH2	ARG- 238	2.84	177.16	H-Bond (Protein Donor)	false
O18	CZ	ARG- 238	3.57	0	Ionic (Protein Cationic)	false
O17	CZ	ARG- 238	3.66	0	Ionic (Protein Cationic)	false
C4	CG	GLN- 242	3.72	0	Hydrophobic	false
CL1	CZ2	TRP- 244	3.46	0	Hydrophobic	false
O13	MN	MN- 702	2.11	0	Metal Acceptor	false
N8	MN	MN- 702	2.2	0	Metal Acceptor	false
DuAr	MN	MN- 702	3.58	88.7	Pi/Cation	false