scPDB - 4p63 entry

Protein Data Bank Entry:

PDB ID : 4p63

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2014-03-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable deoxyhypusine synthase
ID:	DHYS_PYRHO
AC:	O50105
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	2.5.1.46

Chains:

Chain Name:	Percentage of Residues within binding site
A	15 %
C	2 %
D	83 %

Ligand binding site composition:

B-Factor:	42.403
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.243	2484.000

% Hydrophobic	% Polar
38.45	61.55
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	62.95 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
6.60605	5.83084	-16.2481

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
O2N	N	SER- 75	2.88	172.16	H-Bond (Protein Donor)	false
O2N	OG	SER- 75	3.15	135.01	H-Bond (Protein Donor)	false
C2D	CB	SER- 75	4.29	0	Hydrophobic	false
C3N	CB	SER- 75	4.09	0	Hydrophobic	false
N7A	ND2	ASN- 76	3.3	172.78	H-Bond (Protein Donor)	false
O2N	OG1	THR- 101	3.21	164.57	H-Bond (Protein Donor)	false
C3D	CB	THR- 101	3.57	0	Hydrophobic	false
O2D	N	GLY- 103	2.87	154.52	H-Bond (Protein Donor)	false
O3D	OD1	ASP- 214	3.18	137.34	H-Bond (Ligand Donor)	false
O3D	OD2	ASP- 214	2.67	128.32	H-Bond (Ligand Donor)	false
O4B	N	GLY- 261	3.24	155.55	H-Bond (Protein Donor)	false
C5B	CB	SER- 262	4.17	0	Hydrophobic	false
C3D	CD2	LEU- 263	4.08	0	Hydrophobic	false
C4D	CB	HIS- 266	3.62	0	Hydrophobic	false
O2B	N	THR- 286	3.49	122.1	H-Bond (Protein Donor)	false
N3A	N	THR- 286	3.3	138.46	H-Bond (Protein Donor)	false
O2B	OG1	THR- 286	2.76	161.77	H-Bond (Ligand Donor)	false
C2B	CB	ALA- 287	4.36	0	Hydrophobic	false
C4B	CB	SER- 295	4.48	0	Hydrophobic	false
N6A	OD1	ASP- 320	3.24	142.69	H-Bond (Ligand Donor)	false
N1A	N	ALA- 321	2.9	163.57	H-Bond (Protein Donor)	false
O3B	O3B	NAD- 401	2.57	135.99	H-Bond (Ligand Donor)	false