scPDB - 4d8n entry

Protein Data Bank Entry:

PDB ID : 4d8n

Resolution :1.680 Å

Experimental Method : X-ray

Deposition Date : 2012-01-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Kallikrein-6
ID:	KLK6_HUMAN
AC:	Q92876
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.21

Chains:

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

Ligand binding site composition:

B-Factor:	21.230
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.440	297.000

% Hydrophobic	% Polar
37.50	62.50
According to VolSite

Ligand :

HET Code:	0HM
Formula:	C24H25N5O2
Molecular weight:	415.488 g/mol
DrugBank ID:	-
Buried Surface Area:	58.83 %
Polar Surface area:	98.67 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
26.3616	8.60861	36.3375

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
CAR	SG	CYS- 42	3.66	0	Hydrophobic	false
DuAr	DuAr	HIS- 57	3.69	0	Aromatic Face/Face	false
NBC	OD1	ASP- 189	2.95	151.7	H-Bond (Ligand Donor)	false
NBC	OD2	ASP- 189	3.41	149.43	H-Bond (Ligand Donor)	false
NBC	OD1	ASP- 189	2.95	0	Ionic (Ligand Cationic)	false
NBC	OD2	ASP- 189	3.41	0	Ionic (Ligand Cationic)	false
CAZ	CB	SER- 190	4.12	0	Hydrophobic	false
NBC	OG	SER- 190	2.79	149.59	H-Bond (Ligand Donor)	false
OBE	N	GLY- 193	2.6	152.25	H-Bond (Protein Donor)	false
OBE	N	SER- 195	3.1	157.88	H-Bond (Protein Donor)	false
NAT	OG	SER- 195	2.8	148.96	H-Bond (Ligand Donor)	false
CAP	CB	SER- 195	3.4	0	Hydrophobic	false
CAY	CG1	VAL- 213	3.63	0	Hydrophobic	false
CAL	CB	TRP- 215	4.36	0	Hydrophobic	false
CAB	CB	TRP- 215	3.66	0	Hydrophobic	false
CAW	CD1	ILE- 218	4.08	0	Hydrophobic	false
CAV	CG1	ILE- 218	3.93	0	Hydrophobic	false
CAC	CD1	ILE- 218	3.79	0	Hydrophobic	false
CAV	SG	CYS- 220	3.51	0	Hydrophobic	false