scPDB - 2xyd entry

Protein Data Bank Entry:

PDB ID : 2xyd

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2010-11-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.820	8.370	8.400	0.840	9.190	7

List of CHEMBLId :

CHEMBL570953

Binding Site :

Uniprot Annotation

Name:	Angiotensin-converting enzyme
ID:	ACE_HUMAN
AC:	P12821
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.2.1

Chains:

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

Ligand binding site composition:

B-Factor:	26.534
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.222	2544.750

% Hydrophobic	% Polar
34.75	65.25
According to VolSite

Ligand :

HET Code:	3ES
Formula:	C38H36N3O9P
Molecular weight:	709.681 g/mol
DrugBank ID:	-
Buried Surface Area:	60.79 %
Polar Surface area:	203.76 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	5
Aromatic rings:	5
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
1.62871	-16.4594	-21.8925

Binding mode :

What is Poseview ?

2D View
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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
O	NE2	GLN- 259	3	154.12	H-Bond (Protein Donor)	false
CAJ	CB	SER- 260	4.47	0	Hydrophobic	false
OAC	NE2	HIS- 331	2.64	171.34	H-Bond (Protein Donor)	false
CBF	CB	ALA- 332	4.39	0	Hydrophobic	false
CAS	CB	SER- 333	3.72	0	Hydrophobic	false
OAB	N	ALA- 334	2.76	175.72	H-Bond (Protein Donor)	false
CAJ	CB	ASP- 354	3.97	0	Hydrophobic	false
CBB	CB	HIS- 365	4.29	0	Hydrophobic	false
DuAr	DuAr	HIS- 388	3.77	0	Aromatic Face/Face	false
CAK	CB	HIS- 388	3.53	0	Hydrophobic	false
OH	OD2	ASP- 393	3.25	143.33	H-Bond (Ligand Donor)	false
CB	CZ	PHE- 435	3.86	0	Hydrophobic	false
OXT	NZ	LYS- 489	3.79	0	Ionic (Protein Cationic)	false
O	NZ	LYS- 489	2.62	0	Ionic (Protein Cationic)	false
O	NZ	LYS- 489	2.62	166.69	H-Bond (Protein Donor)	false
CAN	CG2	THR- 496	3.73	0	Hydrophobic	false
O	OH	TYR- 498	2.58	152.6	H-Bond (Protein Donor)	false
CB	CZ	TYR- 498	4.11	0	Hydrophobic	false
OAD	OH	TYR- 501	2.53	161.89	H-Bond (Protein Donor)	false
CB	CD1	TYR- 501	3.61	0	Hydrophobic	false
CD2	CD1	TYR- 501	3.46	0	Hydrophobic	false
OAG	ZN	ZN- 1620	2.34	0	Metal Acceptor	false
OAD	ZN	ZN- 1620	2.23	0	Metal Acceptor	false