scPDB - 4tmn entry

Protein Data Bank Entry:

PDB ID : 4tmn

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 1987-06-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
E	100 %

Ligand binding site composition:

B-Factor:	12.592
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.328	438.750

% Hydrophobic	% Polar
42.31	57.69
According to VolSite

Ligand :

HET Code:	0PK
Formula:	C25H32N3O7P
Molecular weight:	517.511 g/mol
DrugBank ID:	-
Buried Surface Area:	53.83 %
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
51.2347	18.2638	-6.98131

Binding mode :

What is Poseview ?

2D View
3D View

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
N2	OD1	ASN- 112	3.07	165.55	H-Bond (Ligand Donor)	false
O3	ND2	ASN- 112	3	169.8	H-Bond (Protein Donor)	false
N1	O	ALA- 113	2.87	130.18	H-Bond (Ligand Donor)	false
CD1	CB	PHE- 114	3.75	0	Hydrophobic	false
O1	N	TRP- 115	2.89	162.4	H-Bond (Protein Donor)	false
CD21	CZ	PHE- 130	4.27	0	Hydrophobic	false
CD21	CD2	LEU- 133	3.89	0	Hydrophobic	false
CD11	CG2	VAL- 139	4.05	0	Hydrophobic	false
CD21	CG2	VAL- 139	3.81	0	Hydrophobic	false
CD11	CB	HIS- 142	4.41	0	Hydrophobic	false
N1	OE2	GLU- 143	3.28	132	H-Bond (Ligand Donor)	false
C2	CB	HIS- 146	3.98	0	Hydrophobic	false
C2	CE2	TYR- 157	4.23	0	Hydrophobic	false
C4	CG	TYR- 157	3.46	0	Hydrophobic	false
C5	CB	TYR- 157	3.61	0	Hydrophobic	false
N	OH	TYR- 157	3.28	132.03	H-Bond (Ligand Donor)	false
CD11	CG2	ILE- 188	4.14	0	Hydrophobic	false
CB2	CD2	LEU- 202	4.05	0	Hydrophobic	false
CG1	CD2	LEU- 202	3.65	0	Hydrophobic	false
O	NH1	ARG- 203	2.82	146.83	H-Bond (Protein Donor)	false
O	NH2	ARG- 203	2.85	145.13	H-Bond (Protein Donor)	false
O1P	NE2	HIS- 231	2.7	171.09	H-Bond (Protein Donor)	false
O1P	ZN	ZN- 322	2.17	0	Metal Acceptor	false
O2P	ZN	ZN- 322	2.59	0	Metal Acceptor	false