scPDB - 3evj entry

Protein Data Bank Entry:

PDB ID : 3evj

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2008-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Antithrombin-III
ID:	ANT3_HUMAN
AC:	P01008
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	75.341
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.019	317.250

% Hydrophobic	% Polar
53.19	46.81
According to VolSite

Ligand :

HET Code:	NTO
Formula:	C31H43N3O49S8
Molecular weight:	1498.184 g/mol
DrugBank ID:	-
Buried Surface Area:	26.43 %
Polar Surface area:	900.81 Å2

Number of
H-Bond Acceptors:	49
H-Bond Donors:	9
Rings:	5
Aromatic rings:	0
Anionic atoms:	10
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	30

Mass center Coordinates

X	Y	Z
62.1117	1.52159	12.3283

Binding mode :

What is Poseview ?

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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
C3F	CG	LYS- 11	4.32	0	Hydrophobic	false
O3J	N	ARG- 13	2.59	138.11	H-Bond (Protein Donor)	false
O3K	CZ	ARG- 13	3.48	0	Ionic (Protein Cationic)	false
C12	CB	ALA- 43	3.95	0	Hydrophobic	false
O16	N	ASN- 45	3.43	125.12	H-Bond (Protein Donor)	false
O18	N	ASN- 45	2.97	172.09	H-Bond (Protein Donor)	false
O24	ND2	ASN- 45	2.88	126.88	H-Bond (Protein Donor)	false
O3D	ND2	ASN- 45	3.31	132.95	H-Bond (Protein Donor)	false
O3E	ND2	ASN- 45	3.3	166.47	H-Bond (Protein Donor)	false
C1K	CB	ASN- 45	4.22	0	Hydrophobic	false
C20	CB	ASN- 45	4.16	0	Hydrophobic	false
C15	CB	ASN- 45	4.36	0	Hydrophobic	false
O45	CZ	ARG- 47	3.49	0	Ionic (Protein Cationic)	false
O45	NH2	ARG- 47	2.55	136.19	H-Bond (Protein Donor)	false
O5I	NH1	ARG- 47	3.25	151.85	H-Bond (Protein Donor)	false
O42	NZ	LYS- 114	2.9	139.47	H-Bond (Protein Donor)	false
O5J	N	LYS- 114	2.74	144	H-Bond (Protein Donor)	false
C50	CG	LYS- 114	4.35	0	Hydrophobic	false
C5F	CB	LYS- 114	4.2	0	Hydrophobic	false
O18	NH1	ARG- 129	2.51	125.55	H-Bond (Protein Donor)	false
O18	CZ	ARG- 129	3.71	0	Ionic (Protein Cationic)	false