scPDB - 1raf entry

Protein Data Bank Entry:

PDB ID : 1raf

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1992-08-14

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
D	100 %

Ligand binding site composition:

B-Factor:	46.386
Number of residues:	21
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.188	249.750

% Hydrophobic	% Polar
51.35	48.65
According to VolSite

Ligand :

HET Code:	CTP
Formula:	C9H12N3O14P3
Molecular weight:	479.125 g/mol
DrugBank ID:	DB02431
Buried Surface Area:	48.12 %
Polar Surface area:	308.95 Å2

Number of
H-Bond Acceptors:	16
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
28.676	94.9146	43.732

Binding mode :

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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
N3	N	ILE- 12	3.33	132.42	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 17	3.78	0	Hydrophobic	false
C4'	CG1	VAL- 17	4.2	0	Hydrophobic	false
O2G	OG1	THR- 82	2.93	176.25	H-Bond (Protein Donor)	false
C5'	CB	ASN- 84	4.29	0	Hydrophobic	false
C1'	CD1	ILE- 86	4.08	0	Hydrophobic	false
N4	O	TYR- 89	2.73	158.19	H-Bond (Ligand Donor)	false
C5'	CG2	VAL- 91	3.69	0	Hydrophobic	false
O2G	NZ	LYS- 94	2.73	137.17	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 94	3.2	147.75	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 94	2.73	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 94	3.2	0	Ionic (Protein Cationic)	false