scPDB - 1d3p entry

Protein Data Bank Entry:

PDB ID : 1d3p

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1999-09-30

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
B	100 %

Ligand binding site composition:

B-Factor:	24.717
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.766	702.000

% Hydrophobic	% Polar
44.23	55.77
According to VolSite

Ligand :

HET Code:	BT3
Formula:	C32H39N3O3S
Molecular weight:	545.735 g/mol
DrugBank ID:	-
Buried Surface Area:	52.14 %
Polar Surface area:	88.7 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-19.0797	-34.5297	20.7157

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
C24	CH2	TRP- 86	3.68	0	Hydrophobic	false
C25	CZ2	TRP- 86	4.3	0	Hydrophobic	false
C29	CB	TRP- 86	4.02	0	Hydrophobic	false
C30	CE3	TRP- 86	4.35	0	Hydrophobic	false
C17	CG	LEU- 132	3.81	0	Hydrophobic	false
C32	CD1	LEU- 132	3.73	0	Hydrophobic	false
C23	CG2	ILE- 215	4.03	0	Hydrophobic	false
O1	OD1	ASP- 235	2.75	122.46	H-Bond (Ligand Donor)	false
C1	CB	ALA- 236	3.96	0	Hydrophobic	false
C10	CB	GLU- 238	4.04	0	Hydrophobic	false
C14	CG	GLU- 238	3.57	0	Hydrophobic	false
C5	CB	SER- 241	4.29	0	Hydrophobic	false
C7	CB	SER- 241	3.84	0	Hydrophobic	false
C6	CG1	VAL- 261	3.53	0	Hydrophobic	false
C23	CD2	TRP- 263	3.79	0	Hydrophobic	false
C11	CB	TRP- 263	3.99	0	Hydrophobic	false
S1	SG	CYS- 267	3.68	0	Hydrophobic	false
C3	SG	CYS- 267	4.47	0	Hydrophobic	false
O1	O	HOH- 569	3.22	126.42	H-Bond (Ligand Donor)	false