scPDB - 4du6 entry

Protein Data Bank Entry:

PDB ID : 4du6

Resolution :2.110 Å

Experimental Method : X-ray

Deposition Date : 2012-02-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GTP cyclohydrolase 1
ID:	GCH1_YERPE
AC:	Q8ZG15
Organism:	Yersinia pestis
Reign:	Bacteria
TaxID:	632
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
D	50 %
E	50 %

Ligand binding site composition:

B-Factor:	61.555
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.600	313.875

% Hydrophobic	% Polar
51.61	48.39
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	62.89 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
79.6652	31.0802	-12.2866

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	OG1	THR- 86	2.58	163.23	H-Bond (Protein Donor)	false
C5'	CB	HIS- 111	3.99	0	Hydrophobic	false
O2B	NE2	HIS- 112	3.06	161.31	H-Bond (Protein Donor)	false
N2	O	ILE- 131	2.83	154.39	H-Bond (Ligand Donor)	false
N3	N	LEU- 133	3.15	159.06	H-Bond (Protein Donor)	false
O2G	OG	SER- 134	3.13	131.32	H-Bond (Protein Donor)	false
O3G	OG	SER- 134	2.84	120.58	H-Bond (Protein Donor)	false
O3'	N	SER- 134	3.4	137.05	H-Bond (Protein Donor)	false
O2'	N	SER- 134	2.98	145.83	H-Bond (Protein Donor)	false
O3'	OG	SER- 134	2.59	151.28	H-Bond (Ligand Donor)	false
O2'	OG	SER- 134	3.16	156.7	H-Bond (Ligand Donor)	false
C3'	CB	SER- 134	4.34	0	Hydrophobic	false
O2G	NZ	LYS- 135	2.59	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 135	3.77	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 135	3.37	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 135	2.66	157.1	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 138	3.53	0	Ionic (Protein Cationic)	false
O2G	CZ	ARG- 138	3.17	0	Ionic (Protein Cationic)	false
O6	N	GLN- 150	2.58	172.99	H-Bond (Protein Donor)	false
N1	OE1	GLU- 151	2.55	173.39	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 151	3.42	124.37	H-Bond (Ligand Donor)	false
C2'	SG	CYS- 180	3.71	0	Hydrophobic	false
O1G	CZ	ARG- 184	3.04	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 184	3.69	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 184	3.87	0	Ionic (Protein Cationic)	false
O1G	NH2	ARG- 184	2.7	134.16	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 184	2.62	137.48	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 184	2.65	138.84	H-Bond (Protein Donor)	false