scPDB - 2z1m entry

Protein Data Bank Entry:

PDB ID : 2z1m

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-05-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-mannose 4,6-dehydratase
ID:	O67175_AQUAE
AC:	O67175
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.689
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.003	577.125

% Hydrophobic	% Polar
41.52	58.48
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	70.76 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
129.753	-0.251607	51.022

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
O3B	ND2	ASN- 180	3.22	161.12	H-Bond (Protein Donor)	false
N2	O	GLU- 189	3.15	139.88	H-Bond (Ligand Donor)	false
O1A	N	VAL- 191	2.79	153.01	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 191	3.77	0	Hydrophobic	false
O6	NZ	LYS- 194	2.63	141.67	H-Bond (Protein Donor)	false
N7	N	GLY- 213	2.66	161.24	H-Bond (Protein Donor)	false
C1'	CB	ALA- 217	4.34	0	Hydrophobic	false
C4'	CB	ALA- 217	4.07	0	Hydrophobic	false
O3B	NE	ARG- 219	3.42	173.79	H-Bond (Protein Donor)	false
C5'	CG	ARG- 219	4.4	0	Hydrophobic	false
C4'	CG2	VAL- 253	4.22	0	Hydrophobic	false
C1'	CG2	VAL- 253	4.16	0	Hydrophobic	false
O2B	NH1	ARG- 297	2.67	151.46	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 297	3.28	137.58	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 297	3.7	0	Ionic (Protein Cationic)	false
C2'	CD	ARG- 297	4.3	0	Hydrophobic	false
O3'	OE1	GLU- 300	2.96	144.19	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 300	2.74	140.14	H-Bond (Ligand Donor)	false
O2B	O	HOH- 1032	2.54	163.81	H-Bond (Protein Donor)	false
O1A	O	HOH- 1083	2.68	179.96	H-Bond (Protein Donor)	false