scPDB - 4ebf entry

Protein Data Bank Entry:

PDB ID : 4ebf

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-03-23

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
C	100 %

Ligand binding site composition:

B-Factor:	38.636
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.998	1623.375

% Hydrophobic	% Polar
42.20	57.80
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	54.62 %
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
14.7119	7.0242	62.8986

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	4.25	0	Hydrophobic	false
C4N	CG2	THR- 104	3.56	0	Hydrophobic	false
O3B	N	MET- 153	2.97	146.95	H-Bond (Protein Donor)	false
O1A	N	ALA- 155	3.03	176.45	H-Bond (Protein Donor)	false
O2N	N	ILE- 156	2.97	167.46	H-Bond (Protein Donor)	false
C5D	CG2	ILE- 156	4.08	0	Hydrophobic	false
C1B	CB	ALA- 175	4.18	0	Hydrophobic	false
C2B	CB	ALA- 176	4.36	0	Hydrophobic	false
O2B	N	ALA- 176	3.18	133.64	H-Bond (Protein Donor)	false
C1B	CB	LEU- 208	4.39	0	Hydrophobic	false
C5B	CG	PRO- 209	4.37	0	Hydrophobic	false
N7N	O	PRO- 235	3.12	155.77	H-Bond (Ligand Donor)	false
C4D	SG	CYS- 236	3.89	0	Hydrophobic	false
N7N	OD1	ASP- 261	2.99	154.8	H-Bond (Ligand Donor)	false
O2N	O	HOH- 913	2.57	179.98	H-Bond (Protein Donor)	false