scPDB - 3wiy entry

Protein Data Bank Entry:

PDB ID : 3wiy

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2013-09-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Induced myeloid leukemia cell differentiation protein Mcl-1
ID:	MCL1_HUMAN
AC:	Q07820
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	66 %
D	27 %
E	5 %

Ligand binding site composition:

B-Factor:	32.691
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.727	411.750

% Hydrophobic	% Polar
81.97	18.03
According to VolSite

Ligand :

HET Code:	LC6
Formula:	C47H46N6O8S2
Molecular weight:	887.034 g/mol
DrugBank ID:	-
Buried Surface Area:	42.63 %
Polar Surface area:	225.86 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	7
Aromatic rings:	7
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
-1.32033	9.99014	10.3111

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
C38	CB	HIS- 224	4.02	0	Hydrophobic	false
C17	CB	ALA- 227	3.65	0	Hydrophobic	false
C17	CB	ALA- 227	3.65	0	Hydrophobic	false
C38	CE1	PHE- 228	3.6	0	Hydrophobic	false
C6	SD	MET- 231	4.5	0	Hydrophobic	false
C9	CD1	LEU- 235	3.67	0	Hydrophobic	false
C7	CD1	LEU- 246	4.25	0	Hydrophobic	false
C6	CB	VAL- 249	4.2	0	Hydrophobic	false
C20	CG	MET- 250	3.89	0	Hydrophobic	false
C27	CG	MET- 250	3.98	0	Hydrophobic	false
C7	CE	MET- 250	3.81	0	Hydrophobic	false
C12	CG1	VAL- 253	3.74	0	Hydrophobic	false
C45	CG1	VAL- 253	3.65	0	Hydrophobic	false
C41	CD1	PHE- 254	4.47	0	Hydrophobic	false
C42	CB	PHE- 254	3.83	0	Hydrophobic	false
O56	CZ	ARG- 263	3.28	0	Ionic (Protein Cationic)	false
O56	NH1	ARG- 263	2.85	141.5	H-Bond (Protein Donor)	false
O56	NE	ARG- 263	2.9	142.55	H-Bond (Protein Donor)	false
C41	CG2	THR- 266	4.06	0	Hydrophobic	false
C41	CB	LEU- 267	4.08	0	Hydrophobic	false
C8	CD1	LEU- 267	3.66	0	Hydrophobic	false
C42	CD1	LEU- 267	4.11	0	Hydrophobic	false
C8	CB	PHE- 270	4.33	0	Hydrophobic	false
C20	CD2	PHE- 270	3.35	0	Hydrophobic	false
C2	CG2	VAL- 274	4.32	0	Hydrophobic	false
C2	CD1	LEU- 290	4.09	0	Hydrophobic	false
C2	CD1	ILE- 294	4.08	0	Hydrophobic	false
C3	CG1	ILE- 294	3.89	0	Hydrophobic	false