scPDB - 3clx entry

Protein Data Bank Entry:

PDB ID : 3clx

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2008-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	E3 ubiquitin-protein ligase XIAP
ID:	XIAP_HUMAN
AC:	P98170
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	6.3.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	20 %
C	40 %
D	40 %

Ligand binding site composition:

B-Factor:	24.843
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.083	2706.750

% Hydrophobic	% Polar
40.40	59.60
According to VolSite

Ligand :

HET Code:	X22
Formula:	C28H37N4O4
Molecular weight:	493.618 g/mol
DrugBank ID:	-
Buried Surface Area:	56.72 %
Polar Surface area:	126.38 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
9.88811	44.6488	-11.4018

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
CAV	CE3	TRP- 323	4.08	0	Hydrophobic	false
CAK	CZ3	TRP- 323	3.43	0	Hydrophobic	false
CAV	CE2	TYR- 324	4.13	0	Hydrophobic	false
CAG	CB	PRO- 325	4.23	0	Hydrophobic	false
CAM	CG	PRO- 325	3.96	0	Hydrophobic	false
OAF	OE1	GLU- 337	2.91	150.24	H-Bond (Ligand Donor)	false
CAR	CD1	TYR- 338	4.31	0	Hydrophobic	false
CAG	CG2	ILE- 339	3.51	0	Hydrophobic	false
CAS	CB	ASN- 341	4.2	0	Hydrophobic	false
CAP	CB	HIS- 343	3.61	0	Hydrophobic	false
CAM	CB	HIS- 343	3.64	0	Hydrophobic	false
CAU	CD2	LEU- 344	4.25	0	Hydrophobic	false
CAL	CD2	LEU- 344	3.76	0	Hydrophobic	false
CAP	CG	LEU- 344	3.96	0	Hydrophobic	false
CAT	CD1	LEU- 344	4.22	0	Hydrophobic	false
CAU	CG2	THR- 345	4.27	0	Hydrophobic	false
CAH	CB	SER- 347	3.67	0	Hydrophobic	false