scPDB - 4fyx entry

Protein Data Bank Entry:

PDB ID : 4fyx

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2012-07-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aspartate carbamoyltransferase regulatory chain
ID:	PYRI_ECOLI
AC:	P0A7F3
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	91 %
D	9 %

Ligand binding site composition:

B-Factor:	53.367
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.349	418.500

% Hydrophobic	% Polar
54.84	45.16
According to VolSite

Ligand :

HET Code:	UTP
Formula:	C9H11N2O15P3
Molecular weight:	480.109 g/mol
DrugBank ID:	DB04005
Buried Surface Area:	57.48 %
Polar Surface area:	299.67 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
11.8844	81.2602	33.7503

Binding mode :

What is Poseview ?

2D View
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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'	NZ	LYS- 6	2.81	124.41	H-Bond (Protein Donor)	false
C2'	CG	LYS- 6	3.68	0	Hydrophobic	false
C2'	CD2	LEU- 7	4.3	0	Hydrophobic	false
O2'	N	LEU- 7	3.23	125.29	H-Bond (Protein Donor)	false
O2	N	VAL- 9	2.92	169.96	H-Bond (Protein Donor)	false
N3	O	VAL- 9	2.89	163.13	H-Bond (Ligand Donor)	false
O3G	NE2	HIS- 20	2.73	167.43	H-Bond (Protein Donor)	false
C4'	CB	LEU- 48	4.38	0	Hydrophobic	false
C1'	CD1	LEU- 48	3.88	0	Hydrophobic	false
C4'	CG	PRO- 49	3.83	0	Hydrophobic	false
O2G	OG	SER- 50	3.5	122.29	H-Bond (Protein Donor)	false
O2G	N	GLU- 52	2.68	150.57	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 56	2.63	147.69	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 56	3.26	130.67	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 56	2.86	157.93	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 56	2.63	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 56	2.86	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 56	3.87	0	Ionic (Protein Cationic)	false
O4	NZ	LYS- 60	2.85	141.04	H-Bond (Protein Donor)	false
O1B	MG	MG- 204	2.14	0	Metal Acceptor	false
O3G	MG	MG- 204	2.03	0	Metal Acceptor	false