scPDB - 5ees entry

Protein Data Bank Entry:

PDB ID : 5ees

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2015-10-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-hydroxy-tetrahydrodipicolinate reductase
ID:	DAPB_CORGL
AC:	P40110
Organism:	Corynebacterium glutamicum
Reign:	Bacteria
TaxID:	196627
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	53.804
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.011	283.500

% Hydrophobic	% Polar
35.71	64.29
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	53.39 %
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
44.1632	22.3858	10.1235

Binding mode :

What is Poseview ?

2D View
3D View

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	N	ARG- 13	2.71	175.85	H-Bond (Protein Donor)	false
O2N	NE	ARG- 13	3.1	130.87	H-Bond (Protein Donor)	false
O2N	NH1	ARG- 13	2.81	138.16	H-Bond (Protein Donor)	false
O2N	CZ	ARG- 13	3.36	0	Ionic (Protein Cationic)	false
O1N	N	VAL- 14	2.94	167.33	H-Bond (Protein Donor)	false
C5N	CG2	VAL- 14	3.83	0	Hydrophobic	false
C5D	CB	PHE- 54	4.14	0	Hydrophobic	false
C4D	CD1	PHE- 54	4.38	0	Hydrophobic	false
N7N	O	GLY- 77	2.98	159.05	H-Bond (Ligand Donor)	false
O3D	N	THR- 79	3.4	164.49	H-Bond (Protein Donor)	false
O2D	OG1	THR- 79	2.95	162.15	H-Bond (Protein Donor)	false
C2D	CG2	THR- 79	4.4	0	Hydrophobic	false
N7N	O	ALA- 104	3.01	138.64	H-Bond (Ligand Donor)	false
O7N	N	PHE- 107	2.88	142.54	H-Bond (Protein Donor)	false
O1N	O	HOH- 407	2.53	167.29	H-Bond (Protein Donor)	false