scPDB - 4d9m entry

Protein Data Bank Entry:

PDB ID : 4d9m

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2012-01-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diaminopropionate ammonia-lyase
ID:	DPAL_ECOLI
AC:	P66899
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	4.3.1.15

Chains:

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

Ligand binding site composition:

B-Factor:	49.975
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.968	702.000

% Hydrophobic	% Polar
46.15	53.85
According to VolSite

Ligand :

HET Code:	0JO
Formula:	C11H10N2O7P
Molecular weight:	313.180 g/mol
DrugBank ID:	-
Buried Surface Area:	77.69 %
Polar Surface area:	167.84 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
25.9852	58.4224	75.0987

Binding mode :

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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
C2A	CE1	PHE- 76	4.38	0	Hydrophobic	false
OP3	NZ	LYS- 77	3.93	0	Ionic (Protein Cationic)	false
OP1	NZ	LYS- 77	3.43	0	Ionic (Protein Cationic)	false
OP1	NZ	LYS- 77	3.43	158.13	H-Bond (Protein Donor)	false
O	OG1	THR- 119	2.55	157.96	H-Bond (Protein Donor)	false
O	N	ASP- 120	3.38	149.28	H-Bond (Protein Donor)	false
O3	ND2	ASN- 122	2.67	162.19	H-Bond (Protein Donor)	false
OXT	N	HIS- 123	2.81	154.78	H-Bond (Protein Donor)	false
OP2	N	GLY- 232	2.69	162.67	H-Bond (Protein Donor)	false
OP3	N	VAL- 233	3.25	162.97	H-Bond (Protein Donor)	false
OP2	N	GLY- 234	2.84	148.96	H-Bond (Protein Donor)	false
OP1	N	MET- 236	2.81	154.69	H-Bond (Protein Donor)	false
C5A	CD2	LEU- 289	3.74	0	Hydrophobic	false
C2A	CB	SER- 339	4.1	0	Hydrophobic	false
C2A	CB	THR- 376	3.58	0	Hydrophobic	false
N1	OG1	THR- 376	2.74	163.08	H-Bond (Protein Donor)	false
C2A	CB	GLU- 377	3.41	0	Hydrophobic	false