scPDB - 6req entry

Protein Data Bank Entry:

PDB ID : 6req

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1998-09-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methylmalonyl-CoA mutase large subunit
ID:	MUTB_PROFR
AC:	P11653
Organism:	Propionibacterium freudenreichii subsp. shermanii
Reign:	Bacteria
TaxID:	1752
EC Number:	5.4.99.2

Chains:

Chain Name:	Percentage of Residues within binding site
C	96 %
D	4 %

Ligand binding site composition:

B-Factor:	22.622
Number of residues:	56
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.230	529.875

% Hydrophobic	% Polar
33.12	66.88
According to VolSite

Ligand :

HET Code:	3CP
Formula:	C25H37N7O18P3S
Molecular weight:	848.584 g/mol
DrugBank ID:	-
Buried Surface Area:	62.44 %
Polar Surface area:	452.74 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	23

Mass center Coordinates

X	Y	Z
-26.856	105.726	45.3806

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
N3	NH1	ARG- 45	2.85	130.77	H-Bond (Protein Donor)	false
C2'	CZ	TYR- 75	4.28	0	Hydrophobic	false
O11	OH	TYR- 75	2.6	148.05	H-Bond (Protein Donor)	false
N6	OG1	THR- 77	3.2	153.09	H-Bond (Ligand Donor)	false
O4'	NH1	ARG- 82	3.25	151.52	H-Bond (Protein Donor)	false
O6	OG1	THR- 85	3.4	128.39	H-Bond (Protein Donor)	false
O22	OG1	THR- 85	2.63	161.13	H-Bond (Protein Donor)	false
O22	CZ	ARG- 87	3.69	0	Ionic (Protein Cationic)	false
O22	NH2	ARG- 87	2.79	166.04	H-Bond (Protein Donor)	false
S	CE1	TYR- 89	3.4	0	Hydrophobic	false
CS2	CE2	TYR- 89	3.6	0	Hydrophobic	false
CP4	CB	SER- 164	4.03	0	Hydrophobic	false
OP1	OG	SER- 164	3.46	156.5	H-Bond (Protein Donor)	false
CP1	CB	THR- 166	4.34	0	Hydrophobic	false
S	CG2	THR- 166	4.2	0	Hydrophobic	false
CP7	CB	THR- 195	4.36	0	Hydrophobic	false
CP4	CG2	THR- 195	4.17	0	Hydrophobic	false
OP3	OG1	THR- 195	2.77	142.69	H-Bond (Ligand Donor)	false
OS4	NE	ARG- 207	2.59	152.61	H-Bond (Protein Donor)	false
OS4	NH2	ARG- 207	3.21	123.99	H-Bond (Protein Donor)	false
OS5	NH2	ARG- 207	2.84	177.21	H-Bond (Protein Donor)	false
OS4	CZ	ARG- 207	3.27	0	Ionic (Protein Cationic)	false
OS5	CZ	ARG- 207	3.69	0	Ionic (Protein Cationic)	false
CS3	CE2	TYR- 243	3.68	0	Hydrophobic	false
OS4	NE2	HIS- 244	2.65	132.19	H-Bond (Protein Donor)	false
O33	NH1	ARG- 283	3.45	128.58	H-Bond (Protein Donor)	false
O33	NH2	ARG- 283	2.72	174.49	H-Bond (Protein Donor)	false
O33	CZ	ARG- 283	3.52	0	Ionic (Protein Cationic)	false
CP7	CB	SER- 285	4.47	0	Hydrophobic	false
CP9	CB	SER- 285	4.16	0	Hydrophobic	false
CP8	CB	SER- 285	4.18	0	Hydrophobic	false
CS1	CZ	PHE- 287	3.49	0	Hydrophobic	false
CP1	CE2	PHE- 287	3.45	0	Hydrophobic	false
CP8	CB	ARG- 326	4.22	0	Hydrophobic	false
CP9	CB	HIS- 328	4.45	0	Hydrophobic	false
CP4	CB	HIS- 328	3.66	0	Hydrophobic	false
CPB	CB	GLN- 361	4.21	0	Hydrophobic	false
CP9	CB	GLN- 361	4.41	0	Hydrophobic	false
CPB	CB	SER- 362	4.12	0	Hydrophobic	false