scPDB - 4mbs entry

Protein Data Bank Entry:

PDB ID : 4mbs

Resolution :2.710 Å

Experimental Method : X-ray

Deposition Date : 2013-08-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.600	7.600	7.600	0.000	7.600	1

List of CHEMBLId :

CHEMBL1201187

Binding Site :

Uniprot Annotation

Name:	C-C chemokine receptor type 5
ID:	CCR5_HUMAN
AC:	P51681
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	66.238
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.057	955.125

% Hydrophobic	% Polar
49.82	50.18
According to VolSite

Ligand :

HET Code:	MRV
Formula:	C29H42F2N5O
Molecular weight:	514.673 g/mol
DrugBank ID:	DB04835
Buried Surface Area:	58.66 %
Polar Surface area:	64.25 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
185.775	111.521	22.6629

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
N3	OH	TYR- 37	2.93	158.17	H-Bond (Protein Donor)	false
C1	CD2	TRP- 86	4.38	0	Hydrophobic	false
C14	CE3	TRP- 86	3.61	0	Hydrophobic	false
C6	CE2	TRP- 86	3.68	0	Hydrophobic	false
C9	CH2	TRP- 86	3.9	0	Hydrophobic	false
C14	CD2	TYR- 89	3.49	0	Hydrophobic	false
C11	CZ	TYR- 108	4.43	0	Hydrophobic	false
C20	CE1	TYR- 108	3.71	0	Hydrophobic	false
C6	CE1	TYR- 108	3.97	0	Hydrophobic	false
C27	CB	PHE- 112	4.22	0	Hydrophobic	false
F1	CE2	PHE- 182	3.25	0	Hydrophobic	false
F1	CG	LYS- 191	4.16	0	Hydrophobic	false
F2	CG	LYS- 191	3.67	0	Hydrophobic	false
C24	CB	GLN- 194	4.03	0	Hydrophobic	false
C24	CB	THR- 195	4.45	0	Hydrophobic	false
C25	CD1	ILE- 198	4.46	0	Hydrophobic	false
C22	CD1	ILE- 198	3.71	0	Hydrophobic	false
N5	OH	TYR- 251	3.07	166.92	H-Bond (Ligand Donor)	false
C17	CD1	LEU- 255	4.18	0	Hydrophobic	false
C23	CD1	LEU- 255	3.7	0	Hydrophobic	false
C23	CE	MET- 279	4.02	0	Hydrophobic	false
C19	CB	GLU- 283	3.96	0	Hydrophobic	false
C26	CG	GLU- 283	3.84	0	Hydrophobic	false
N2	OE2	GLU- 283	3.68	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 283	2.87	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 283	2.87	168.4	H-Bond (Ligand Donor)	false
C20	CG	MET- 287	3.85	0	Hydrophobic	false