scPDB - 1d4p entry

Protein Data Bank Entry:

PDB ID : 1d4p

Resolution :2.070 Å

Experimental Method : X-ray

Deposition Date : 1999-10-04

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:	21.084
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.613	648.000

% Hydrophobic	% Polar
40.63	59.38
According to VolSite

Ligand :

HET Code:	BPP
Formula:	C22H25N4O
Molecular weight:	361.460 g/mol
DrugBank ID:	-
Buried Surface Area:	59.6 %
Polar Surface area:	84.28 Å2

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

Mass center Coordinates

X	Y	Z
-19.3634	-33.4386	22.4273

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
C21	CE2	TYR- 83	3.98	0	Hydrophobic	false
C22	CZ	TYR- 83	4.19	0	Hydrophobic	false
C21	CH2	TRP- 86	3.69	0	Hydrophobic	false
C23	CD1	LEU- 132	4.12	0	Hydrophobic	false
C41	CG	LEU- 132	3.72	0	Hydrophobic	false
C39	CG1	ILE- 215	4.14	0	Hydrophobic	false
C40	CG2	ILE- 215	4.24	0	Hydrophobic	false
C13	OD2	ASP- 235	3.57	0	Ionic (Ligand Cationic)	false
C13	OD1	ASP- 235	3.62	0	Ionic (Ligand Cationic)	false
N14	OD1	ASP- 235	2.9	146.08	H-Bond (Ligand Donor)	false
N15	OD2	ASP- 235	2.73	163.38	H-Bond (Ligand Donor)	false
C6	CB	ALA- 236	4.2	0	Hydrophobic	false
C5	CB	SER- 241	4.05	0	Hydrophobic	false
C6	CG1	VAL- 261	3.87	0	Hydrophobic	false
C23	CB	TRP- 263	3.8	0	Hydrophobic	false
N15	O	GLY- 266	2.8	147.19	H-Bond (Ligand Donor)	false