scPDB - 3c3d entry

Protein Data Bank Entry:

PDB ID : 3c3d

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-01-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-phospho-L-lactate transferase
ID:	COFD_METMA
AC:	Q8PVT6
Organism:	Methanosarcina mazei
Reign:	Archaea
TaxID:	192952
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.996
Number of residues:	26
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.427	702.000

% Hydrophobic	% Polar
58.65	41.35
According to VolSite

Ligand :

HET Code:	FO1
Formula:	C16H17N3O7
Molecular weight:	363.322 g/mol
DrugBank ID:	-
Buried Surface Area:	50.3 %
Polar Surface area:	162.91 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-10.8868	73.8122	1.39995

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
C7	CG2	ILE- 43	4.4	0	Hydrophobic	false
C15	CB	PRO- 45	4.12	0	Hydrophobic	false
C11	CB	PRO- 45	3.67	0	Hydrophobic	false
C14	CB	TRP- 64	3.79	0	Hydrophobic	false
C11	CB	TRP- 64	4.02	0	Hydrophobic	false
C6	CD1	LEU- 86	3.75	0	Hydrophobic	false
O2	N	LYS- 87	2.98	170.62	H-Bond (Protein Donor)	false
C6	CD1	LEU- 88	4.22	0	Hydrophobic	false
O10	O	HOH- 407	3.04	158.83	H-Bond (Protein Donor)	false
O10	O	HOH- 445	2.73	157.04	H-Bond (Ligand Donor)	false