scPDB - 4e5p entry

Protein Data Bank Entry:

PDB ID : 4e5p

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-03-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphonate dehydrogenase
ID:	PTXD_PSEST
AC:	O69054
Organism:	Pseudomonas stutzeri
Reign:	Bacteria
TaxID:	316
EC Number:	1.20.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	24.474
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.165	1066.500

% Hydrophobic	% Polar
41.46	58.54
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	55.86 %
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
-48.2842	-5.3857	113.743

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
C5N	CB	LEU- 100	4.11	0	Hydrophobic	false
C3N	CG2	THR- 104	3.74	0	Hydrophobic	false
C4N	CB	THR- 104	3.74	0	Hydrophobic	false
O1A	N	ALA- 155	2.86	169.05	H-Bond (Protein Donor)	false
O2N	N	ILE- 156	2.75	172.58	H-Bond (Protein Donor)	false
C5D	CG1	ILE- 156	4.04	0	Hydrophobic	false
C5N	CD1	ILE- 156	3.82	0	Hydrophobic	false
C1B	CB	ALA- 175	4.37	0	Hydrophobic	false
N3A	N	ARG- 176	3.17	148.77	H-Bond (Protein Donor)	false
O2B	N	LYS- 177	3.1	163.94	H-Bond (Protein Donor)	false
C1B	CD2	LEU- 208	3.89	0	Hydrophobic	false
C5B	CG	PRO- 209	4.17	0	Hydrophobic	false
N7N	O	PRO- 235	3	163.78	H-Bond (Ligand Donor)	false
C4D	SG	CYS- 236	4.05	0	Hydrophobic	false
N7N	OD2	ASP- 261	2.95	160.95	H-Bond (Ligand Donor)	false
O2N	O	HOH- 931	2.8	162.01	H-Bond (Protein Donor)	false