scPDB - 1rpn entry

Protein Data Bank Entry:

PDB ID : 1rpn

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2003-12-03

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:	GM4D_PSEAE
AC:	Q51366
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	89 %
D	11 %

Ligand binding site composition:

B-Factor:	16.705
Number of residues:	71
Including
Standard Amino Acids:	59
Non Standard Amino Acids:	2
Water Molecules:	10
Cofactors:	GDP NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.052	286.875

% Hydrophobic	% Polar
35.29	64.71
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	76.81 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
104.057	42.4673	35.1698

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	OG1	THR- 11	2.94	165.78	H-Bond (Ligand Donor)	false
O2A	N	GLN- 13	3.17	169.48	H-Bond (Protein Donor)	false
O2N	N	ASP- 14	2.79	164.24	H-Bond (Protein Donor)	false
C5D	CB	ASP- 14	3.82	0	Hydrophobic	false
O1A	NH2	ARG- 35	2.96	140.79	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 35	2.81	149.68	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 35	3.31	0	Ionic (Protein Cationic)	false
O1X	CZ	ARG- 36	3.46	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 36	3.41	0	Ionic (Protein Cationic)	false
O1X	NE	ARG- 36	2.54	156.06	H-Bond (Protein Donor)	false
O2X	NH1	ARG- 36	2.71	150.52	H-Bond (Protein Donor)	false
O2X	NE	ARG- 36	3.31	128.65	H-Bond (Protein Donor)	false
O3X	N	SER- 37	2.89	157.71	H-Bond (Protein Donor)	false
O3X	OG	SER- 37	2.52	157.59	H-Bond (Protein Donor)	false
C3B	CB	SER- 37	3.65	0	Hydrophobic	false
N6A	OD1	ASP- 59	2.75	157.68	H-Bond (Ligand Donor)	false
N1A	N	MET- 60	2.86	173.63	H-Bond (Protein Donor)	false
C5D	CB	LEU- 81	3.92	0	Hydrophobic	false
C1B	CB	ALA- 82	4.2	0	Hydrophobic	false
O4B	N	ALA- 83	3.19	155.6	H-Bond (Protein Donor)	false
C3D	CB	ALA- 83	3.71	0	Hydrophobic	false
O1A	OG	SER- 85	2.54	153.46	H-Bond (Protein Donor)	false
O3	OG	SER- 85	3.41	121.61	H-Bond (Protein Donor)	false
C2D	CB	SER- 85	3.43	0	Hydrophobic	false
C4D	CB	ALA- 124	3.53	0	Hydrophobic	false
C5N	CB	THR- 126	3.45	0	Hydrophobic	false
O2D	OH	TYR- 150	2.59	164.58	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 154	2.69	156.75	H-Bond (Protein Donor)	false
C5N	CB	LEU- 177	3.95	0	Hydrophobic	false
O7N	N	HIS- 180	2.89	164.14	H-Bond (Protein Donor)	false
O2A	O	HOH- 1609	2.8	168.94	H-Bond (Protein Donor)	false