scPDB - 1e1c entry

Protein Data Bank Entry:

PDB ID : 1e1c

Resolution :2.620 Å

Experimental Method : X-ray

Deposition Date : 2000-04-30

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
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	29.376
Number of residues:	48
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.207	570.375

% Hydrophobic	% Polar
38.46	61.54
According to VolSite

Ligand :

HET Code:	DCA
Formula:	C21H32N7O16P3
Molecular weight:	731.437 g/mol
DrugBank ID:	DB01829
Buried Surface Area:	61.52 %
Polar Surface area:	387.31 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
24.3625	13.7823	58.2908

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
N3A	NH1	ARG- 45	2.84	128.54	H-Bond (Protein Donor)	false
C2B	CZ	TYR- 75	4.17	0	Hydrophobic	false
O1A	OH	TYR- 75	2.58	154.2	H-Bond (Protein Donor)	false
N6A	OG1	THR- 77	3.37	151.86	H-Bond (Ligand Donor)	false
O4B	NH1	ARG- 82	2.77	139.86	H-Bond (Protein Donor)	false
O3A	OG1	THR- 85	3.43	127.71	H-Bond (Protein Donor)	false
O5A	OG1	THR- 85	2.73	158.15	H-Bond (Protein Donor)	false
O5A	NH2	ARG- 87	2.68	161.38	H-Bond (Protein Donor)	false
O5A	CZ	ARG- 87	3.69	0	Ionic (Protein Cationic)	false
C2P	CD1	TYR- 89	3.91	0	Hydrophobic	false
O5P	OG	SER- 114	3.14	135.88	H-Bond (Protein Donor)	false
C6P	CB	SER- 164	4.25	0	Hydrophobic	false
O5P	OG	SER- 164	2.97	140.02	H-Bond (Protein Donor)	false
C2P	CG2	THR- 166	4.1	0	Hydrophobic	false
CAP	CB	THR- 195	4.32	0	Hydrophobic	false
C6P	CG2	THR- 195	4.36	0	Hydrophobic	false
OAP	OG1	THR- 195	2.7	146.1	H-Bond (Ligand Donor)	false
O9A	CZ	ARG- 283	3.45	0	Ionic (Protein Cationic)	false
O9A	NH2	ARG- 283	2.66	161.98	H-Bond (Protein Donor)	false
O9A	NH1	ARG- 283	3.39	127.32	H-Bond (Protein Donor)	false
CDP	CB	SER- 285	4.43	0	Hydrophobic	false
CEP	CB	SER- 285	4.06	0	Hydrophobic	false
CAP	CB	SER- 285	4.48	0	Hydrophobic	false
C2P	CE2	PHE- 287	3.76	0	Hydrophobic	false
CEP	CB	ARG- 326	4.21	0	Hydrophobic	false
CDP	CB	HIS- 328	4.39	0	Hydrophobic	false
C6P	CB	HIS- 328	3.68	0	Hydrophobic	false
CCP	CB	GLN- 361	4.09	0	Hydrophobic	false
CDP	CB	GLN- 361	4.46	0	Hydrophobic	false