scPDB - 4e5m entry

Protein Data Bank Entry:

PDB ID : 4e5m

Resolution :1.850 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
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	12.592
Number of residues:	49
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.307	452.250

% Hydrophobic	% Polar
58.21	41.79
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	61.05 %
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
-12.1987	25.7887	0.086375

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
O1A	NZ	LYS- 76	3.21	141.95	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 76	2.66	157.84	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 76	3.21	0	Ionic (Protein Cationic)	false
O1N	NZ	LYS- 76	2.66	0	Ionic (Protein Cationic)	false
C3D	CG	LYS- 76	4.24	0	Hydrophobic	false
C5N	CB	LYS- 76	3.93	0	Hydrophobic	false
C4N	CD2	LEU- 100	3.8	0	Hydrophobic	false
C5N	CB	LEU- 100	3.81	0	Hydrophobic	false
C3N	CG2	THR- 104	3.92	0	Hydrophobic	false
C4N	CB	THR- 104	4.04	0	Hydrophobic	false
O1A	N	ALA- 155	2.94	170.43	H-Bond (Protein Donor)	false
O2N	N	ILE- 156	2.86	170.54	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 156	4.21	0	Hydrophobic	false
C5N	CD1	ILE- 156	3.73	0	Hydrophobic	false
O1X	CZ	ARG- 176	3.38	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 176	3.79	0	Ionic (Protein Cationic)	false
O1X	NH1	ARG- 176	2.65	133.32	H-Bond (Protein Donor)	false
O3X	NE	ARG- 176	3.4	143.64	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 176	3.3	145.7	H-Bond (Protein Donor)	false
C1B	CD2	LEU- 208	4.16	0	Hydrophobic	false
C5B	CG	PRO- 209	4.33	0	Hydrophobic	false
N7N	O	PRO- 235	2.87	160.56	H-Bond (Ligand Donor)	false
C4D	CB	CYS- 236	3.9	0	Hydrophobic	false
N7N	OD2	ASP- 261	2.91	172.2	H-Bond (Ligand Donor)	false
O2N	O	HOH- 927	2.67	179.97	H-Bond (Protein Donor)	false
O2D	O	HOH- 1117	2.85	171.27	H-Bond (Protein Donor)	false