scPDB - 1mfz entry

Protein Data Bank Entry:

PDB ID : 1mfz

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2002-08-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-mannose 6-dehydrogenase
ID:	ALGD_PSEAE
AC:	P11759
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	1.1.1.132

Chains:

Chain Name:	Percentage of Residues within binding site
C	45 %
D	55 %

Ligand binding site composition:

B-Factor:	26.876
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.825	637.875

% Hydrophobic	% Polar
41.80	58.20
According to VolSite

Ligand :

HET Code:	GDX
Formula:	C16H20N5O17P2
Molecular weight:	616.301 g/mol
DrugBank ID:	DB04023
Buried Surface Area:	72.21 %
Polar Surface area:	372.61 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	7
Rings:	4
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
125.155	140.51	185.258

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
O3'	O	PHE- 158	3.06	146.56	H-Bond (Ligand Donor)	false
O4'	O	LEU- 159	2.98	159.27	H-Bond (Ligand Donor)	false
C3'	CG	ARG- 160	3.72	0	Hydrophobic	false
O2B	N	GLU- 161	2.97	168.71	H-Bond (Protein Donor)	false
O6A	NZ	LYS- 210	2.8	138.55	H-Bond (Protein Donor)	false
O6A	NZ	LYS- 210	2.8	0	Ionic (Protein Cationic)	false
O6A	ND2	ASN- 214	2.56	152.37	H-Bond (Protein Donor)	false
O2'	ND1	HIS- 217	2.85	150.8	H-Bond (Ligand Donor)	false
C1D	CG2	VAL- 221	4.4	0	Hydrophobic	false
N2	OD1	ASN- 225	3.44	124.84	H-Bond (Ligand Donor)	false
O2A	OH	TYR- 256	2.71	160.36	H-Bond (Protein Donor)	false
C5D	CE1	TYR- 257	4.04	0	Hydrophobic	false
O2'	OH	TYR- 257	3.46	126.49	H-Bond (Ligand Donor)	false
N2	O	ARG- 259	3.07	127.67	H-Bond (Ligand Donor)	false
O6	N	ARG- 259	2.78	151.46	H-Bond (Protein Donor)	false
N2	O	PHE- 262	3.01	173.91	H-Bond (Ligand Donor)	false
C1D	CB	PHE- 264	4.06	0	Hydrophobic	false
C4D	CB	PHE- 264	3.55	0	Hydrophobic	false
O3D	N	GLY- 265	2.74	156.03	H-Bond (Protein Donor)	false
C1'	CB	CYS- 268	4.46	0	Hydrophobic	false
C5'	SG	CYS- 268	3.78	0	Hydrophobic	false
C1'	CD1	LEU- 269	4.18	0	Hydrophobic	false
C5D	CD2	LEU- 269	3.44	0	Hydrophobic	false
C3D	CD2	PHE- 323	3.85	0	Hydrophobic	false
C5D	CE2	PHE- 323	4.25	0	Hydrophobic	false
O2A	NZ	LYS- 324	2.58	144.65	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 324	2.58	0	Ionic (Protein Cationic)	false
O3B	O	HOH- 512	3.13	176.62	H-Bond (Protein Donor)	false