scPDB - 4hnh entry

Protein Data Bank Entry:

PDB ID : 4hnh

Resolution :1.580 Å

Experimental Method : X-ray

Deposition Date : 2012-10-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent epimerase/dehydratase
ID:	D1BQI7_VEIPT
AC:	D1BQI7
Organism:	Veillonella parvula
Reign:	Bacteria
TaxID:	479436
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.825
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.329	590.625

% Hydrophobic	% Polar
44.00	56.00
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	62.35 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-8.70573	27.7103	-27.451

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
O1A	N	GLN- 13	3.07	168.1	H-Bond (Protein Donor)	false
O2N	N	ILE- 14	2.86	170.53	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 14	4.12	0	Hydrophobic	false
DuAr	CZ	ARG- 35	3.92	157.56	Pi/Cation	false
O2X	CZ	ARG- 40	3.61	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 40	3.63	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 40	2.68	168.36	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 40	2.86	151.92	H-Bond (Protein Donor)	false
N1A	N	PHE- 58	2.94	160.55	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 58	3.48	0	Aromatic Face/Face	false
C1B	CB	ALA- 78	4.36	0	Hydrophobic	false
C3D	CB	ALA- 78	4.46	0	Hydrophobic	false
C5B	CB	ALA- 78	4.04	0	Hydrophobic	false
O3D	OE2	GLU- 80	2.76	163.19	H-Bond (Ligand Donor)	false
N6A	OD2	ASP- 84	2.98	142.84	H-Bond (Ligand Donor)	false
C5D	CG2	VAL- 103	3.75	0	Hydrophobic	false
C5N	CB	MET- 105	4.22	0	Hydrophobic	false
O2D	OH	TYR- 128	2.87	148.26	H-Bond (Protein Donor)	false
C5N	CB	LEU- 151	3.68	0	Hydrophobic	false
C3N	CD1	LEU- 154	3.61	0	Hydrophobic	false
C4N	CG	LEU- 154	3.78	0	Hydrophobic	false
C5N	CD1	LEU- 154	4.39	0	Hydrophobic	false
O7N	N	LEU- 154	2.94	165.51	H-Bond (Protein Donor)	false
O1N	NE	ARG- 179	2.89	164.12	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 179	3.47	132.36	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 179	3.61	0	Ionic (Protein Cationic)	false
O3D	O	HOH- 422	2.73	179.95	H-Bond (Protein Donor)	false