scPDB - 1d9i entry

Protein Data Bank Entry:

PDB ID : 1d9i

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1999-10-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prothrombin
ID:	THRB_HUMAN
AC:	P00734
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.21.5

Chains:

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

Ligand binding site composition:

B-Factor:	23.653
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.953	779.625

% Hydrophobic	% Polar
46.75	53.25
According to VolSite

Ligand :

HET Code:	00P
Formula:	C22H30N5O5S
Molecular weight:	476.569 g/mol
DrugBank ID:	-
Buried Surface Area:	57.67 %
Polar Surface area:	143.11 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
17.159	-14.3477	23.3705

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
C14	CH2	TRP- 60	3.36	0	Hydrophobic	false
C14	CZ	TYR- 60	3.59	0	Hydrophobic	false
C17	CD1	LEU- 99	4.32	0	Hydrophobic	false
C37	CG1	ILE- 174	3.49	0	Hydrophobic	false
C38	CG2	ILE- 174	3.74	0	Hydrophobic	false
C39	CD1	ILE- 174	4.12	0	Hydrophobic	false
C36	CD1	ILE- 174	3.46	0	Hydrophobic	false
N2	OD1	ASP- 189	3.17	0	Ionic (Ligand Cationic)	false
N2	OD2	ASP- 189	3.95	0	Ionic (Ligand Cationic)	false
N2	O	ALA- 190	3.4	149.45	H-Bond (Ligand Donor)	false
C4	CB	ALA- 190	3.99	0	Hydrophobic	false
C6	CB	CYS- 191	4.11	0	Hydrophobic	false
C4	CG1	VAL- 213	4.03	0	Hydrophobic	false
C3	CG1	VAL- 213	3.66	0	Hydrophobic	false
C17	CB	TRP- 215	4.13	0	Hydrophobic	false
C32	CE3	TRP- 215	4.25	0	Hydrophobic	false
O13	N	GLY- 216	2.86	161.1	H-Bond (Protein Donor)	false
C32	CG	GLU- 217	3.84	0	Hydrophobic	false
N2	O	GLY- 219	2.91	141.91	H-Bond (Ligand Donor)	false
C6	SG	CYS- 220	3.6	0	Hydrophobic	false