scPDB - 4d9w entry

Protein Data Bank Entry:

PDB ID : 4d9w

Resolution :1.380 Å

Experimental Method : X-ray

Deposition Date : 2012-01-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.270	7.270	7.270	0.000	7.270	1

List of CHEMBLId :

CHEMBL3559407

Binding Site :

Uniprot Annotation

Name:	Thermolysin
ID:	THER_BACTH
AC:	P00800
Organism:	Bacillus thermoproteolyticus
Reign:	Bacteria
TaxID:	1427
EC Number:	3.4.24.27

Chains:

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

Ligand binding site composition:

B-Factor:	9.093
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.144	357.750

% Hydrophobic	% Polar
38.68	61.32
According to VolSite

Ligand :

HET Code:	X32
Formula:	C24H30N3O7P
Molecular weight:	503.485 g/mol
DrugBank ID:	-
Buried Surface Area:	51.13 %
Polar Surface area:	169.52 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
11.1742	41.0317	-5.88823

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
C34	CB	ASN- 111	4.06	0	Hydrophobic	false
N16	OD1	ASN- 112	3.23	152.56	H-Bond (Ligand Donor)	false
O19	ND2	ASN- 112	2.96	172.74	H-Bond (Protein Donor)	false
C33	CB	ASN- 112	3.91	0	Hydrophobic	false
N13	O	ALA- 113	2.88	122.77	H-Bond (Ligand Donor)	false
C28	CE1	PHE- 130	4.25	0	Hydrophobic	false
C33	CE2	PHE- 130	3.34	0	Hydrophobic	false
C28	CD2	LEU- 133	3.79	0	Hydrophobic	false
C27	CG2	VAL- 139	4.12	0	Hydrophobic	false
C28	CG2	VAL- 139	3.84	0	Hydrophobic	false
C27	CB	HIS- 142	4.42	0	Hydrophobic	false
O23	OE1	GLU- 143	2.6	178.01	H-Bond (Protein Donor)	false
N13	OE2	GLU- 143	3.37	137.6	H-Bond (Ligand Donor)	false
C7	CE2	TYR- 157	4.14	0	Hydrophobic	false
N10	OH	TYR- 157	3.38	152.43	H-Bond (Ligand Donor)	false
C27	CG2	ILE- 188	4.1	0	Hydrophobic	false
C30	CD2	LEU- 202	3.81	0	Hydrophobic	false
C26	CD2	LEU- 202	3.69	0	Hydrophobic	false
O29	NH2	ARG- 203	2.9	142.24	H-Bond (Protein Donor)	false
O29	NH1	ARG- 203	2.86	144.38	H-Bond (Protein Donor)	false
O24	NE2	HIS- 231	2.87	174.72	H-Bond (Protein Donor)	false
O24	ZN	ZN- 408	1.99	0	Metal Acceptor	false