scPDB - 5cmx entry

Protein Data Bank Entry:

PDB ID : 5cmx

Resolution :2.980 Å

Experimental Method : X-ray

Deposition Date : 2015-07-17

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
H	100 %

Ligand binding site composition:

B-Factor:	52.856
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.179	617.625

% Hydrophobic	% Polar
50.82	49.18
According to VolSite

Ligand :

HET Code:	0G6
Formula:	C21H35ClN6O3
Molecular weight:	454.994 g/mol
DrugBank ID:	DB06841
Buried Surface Area:	62.04 %
Polar Surface area:	160.91 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	6
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-7.05867	22.7786	-27.0771

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
C3	SG	CYS- 42	4.46	0	Hydrophobic	false
CG1	CH2	TRP- 60	3.89	0	Hydrophobic	false
CG1	CZ	TYR- 60	3.51	0	Hydrophobic	false
CZ	CG	LEU- 99	4.13	0	Hydrophobic	false
CE1	CD1	LEU- 99	3.57	0	Hydrophobic	false
CB1	CD1	LEU- 99	3.68	0	Hydrophobic	false
NH1	OD1	ASP- 189	3.3	175.13	H-Bond (Ligand Donor)	false
NH2	OD2	ASP- 189	3.26	177.87	H-Bond (Ligand Donor)	false
O2	N	GLY- 193	2.96	142.75	H-Bond (Protein Donor)	false
O2	N	SER- 195	3.3	141.82	H-Bond (Protein Donor)	false
CB2	CB	SER- 195	4.16	0	Hydrophobic	false
C3	CB	SER- 195	3.34	0	Hydrophobic	false
CB2	CG1	VAL- 213	4.24	0	Hydrophobic	false
CD3	CG1	VAL- 213	4.34	0	Hydrophobic	false
N2	O	SER- 214	3.14	146.63	H-Bond (Ligand Donor)	false
CB	CE3	TRP- 215	4.18	0	Hydrophobic	false
CD1	CB	TRP- 215	4.14	0	Hydrophobic	false
N	O	GLY- 216	2.79	155.5	H-Bond (Ligand Donor)	false
O	N	GLY- 216	3.25	170.96	H-Bond (Protein Donor)	false
NH2	O	GLY- 219	2.74	141.89	H-Bond (Ligand Donor)	false