scPDB - 3wix entry

Protein Data Bank Entry:

PDB ID : 3wix

Resolution :1.900 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
B	28 %
D	72 %

Ligand binding site composition:

B-Factor:	33.705
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.209	843.750

% Hydrophobic	% Polar
61.20	38.80
According to VolSite

Ligand :

HET Code:	LC3
Formula:	C28H20N2O5
Molecular weight:	464.469 g/mol
DrugBank ID:	-
Buried Surface Area:	77.24 %
Polar Surface area:	106.79 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	5
Aromatic rings:	5
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-23.7653	18.4257	-2.9408

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
C2	CB	PRO- 198	4.21	0	Hydrophobic	false
C2	CB	MET- 199	4.29	0	Hydrophobic	false
O7	N	MET- 199	2.9	172.33	H-Bond (Protein Donor)	false
N16	N	SER- 202	3.1	131.19	H-Bond (Protein Donor)	false
N16	OG	SER- 202	3.23	122.8	H-Bond (Protein Donor)	false
O24	N	SER- 202	3.11	144.99	H-Bond (Protein Donor)	false
O24	OG	SER- 202	2.7	144.13	H-Bond (Protein Donor)	false
C6	CB	SER- 202	4.4	0	Hydrophobic	false
O7	NH2	ARG- 207	2.83	166.18	H-Bond (Protein Donor)	false
O8	NE	ARG- 207	3.15	179.11	H-Bond (Protein Donor)	false
O7	CZ	ARG- 207	3.69	0	Ionic (Protein Cationic)	false
O8	CZ	ARG- 207	3.94	0	Ionic (Protein Cationic)	false
C1	CB	ALA- 227	3.47	0	Hydrophobic	false
C28	CE	MET- 231	3.51	0	Hydrophobic	false
C29	CD1	LEU- 235	4.2	0	Hydrophobic	false
C32	CD1	LEU- 246	4.48	0	Hydrophobic	false
C28	CG1	VAL- 249	3.83	0	Hydrophobic	false
C28	CB	MET- 250	4.39	0	Hydrophobic	false
C26	CG	MET- 250	3.78	0	Hydrophobic	false
C30	CG	MET- 250	3.97	0	Hydrophobic	false
C32	CE	MET- 250	3.66	0	Hydrophobic	false
C31	CG	MET- 250	3.66	0	Hydrophobic	false
C27	CB	VAL- 253	4.32	0	Hydrophobic	false
C22	CG1	VAL- 253	3.51	0	Hydrophobic	false
C21	CD1	PHE- 254	4.13	0	Hydrophobic	false
O25	NH1	ARG- 263	2.75	148.35	H-Bond (Protein Donor)	false
O25	NE	ARG- 263	2.91	141.17	H-Bond (Protein Donor)	false
O25	CZ	ARG- 263	3.24	0	Ionic (Protein Cationic)	false
C20	CG2	THR- 266	4.14	0	Hydrophobic	false
C20	CB	LEU- 267	4.3	0	Hydrophobic	false
C21	CD1	LEU- 267	4.33	0	Hydrophobic	false
C26	CD1	LEU- 267	4.47	0	Hydrophobic	false
C35	CD1	LEU- 267	3.78	0	Hydrophobic	false
C35	CB	PHE- 270	4.18	0	Hydrophobic	false
C33	CD1	LEU- 290	4.05	0	Hydrophobic	false
C34	CD1	ILE- 294	3.9	0	Hydrophobic	false
O24	O	HOH- 906	2.76	179.95	H-Bond (Protein Donor)	false