scPDB - 3mpi entry

Protein Data Bank Entry:

PDB ID : 3mpi

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2010-04-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutaryl-CoA dehydrogenase
ID:	ACD_DESML
AC:	C3UVB0
Organism:	Desulfococcus multivorans
Reign:	Bacteria
TaxID:	897
EC Number:	1.3.99.32

Chains:

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

Ligand binding site composition:

B-Factor:	40.844
Number of residues:	48
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.249	860.625

% Hydrophobic	% Polar
38.04	61.96
According to VolSite

Ligand :

HET Code:	GRA
Formula:	C26H37N7O19P3S
Molecular weight:	876.594 g/mol
DrugBank ID:	-
Buried Surface Area:	56.39 %
Polar Surface area:	469.81 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
-22.0014	65.1715	-16.0665

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
O5	NH1	ARG- 87	2.82	148.99	H-Bond (Protein Donor)	false
O6	NH2	ARG- 87	2.75	139.69	H-Bond (Protein Donor)	false
O5	CZ	ARG- 87	3.64	0	Ionic (Protein Cationic)	false
O6	CZ	ARG- 87	3.49	0	Ionic (Protein Cationic)	false
C10	CG1	VAL- 88	3.98	0	Hydrophobic	false
O5	ND2	ASN- 91	2.85	167.57	H-Bond (Protein Donor)	false
C10	CE	MET- 92	4.01	0	Hydrophobic	false
S1	CE1	PHE- 126	3.49	0	Hydrophobic	false
C6	CD1	ILE- 128	4.09	0	Hydrophobic	false
O1	O	SER- 135	3.07	163.35	H-Bond (Ligand Donor)	false
N1	O	SER- 135	2.93	158.78	H-Bond (Ligand Donor)	false
C3	CG2	VAL- 137	3.5	0	Hydrophobic	false
C5X	CG	MET- 138	4.26	0	Hydrophobic	false
O8A	OG	SER- 181	2.64	164.83	H-Bond (Protein Donor)	false
C4X	CB	SER- 181	3.73	0	Hydrophobic	false
C4X	CB	ALA- 235	4.47	0	Hydrophobic	false
C1X	CD1	PHE- 239	4.25	0	Hydrophobic	false
C14	CE2	PHE- 239	3.61	0	Hydrophobic	false
C5X	CE1	PHE- 239	3.8	0	Hydrophobic	false
C3	CD1	LEU- 242	4.22	0	Hydrophobic	false
C6	CD2	LEU- 242	4.04	0	Hydrophobic	false
O2	NH2	ARG- 246	3.1	162.3	H-Bond (Protein Donor)	false
O3	NH2	ARG- 246	2.9	141.65	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 315	2.91	170.2	H-Bond (Ligand Donor)	false
N1A	ND2	ASN- 315	3.12	171.58	H-Bond (Protein Donor)	false
O4	N	GLU- 367	3.02	144.97	H-Bond (Protein Donor)	false
C10	CG	GLU- 367	4.35	0	Hydrophobic	false
C15	CG2	ILE- 372	3.97	0	Hydrophobic	false
C16	CG2	ILE- 372	4.39	0	Hydrophobic	false
C15	CG1	ILE- 376	3.89	0	Hydrophobic	false
O2A	NE	ARG- 385	3.08	133.85	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 385	2.69	150.55	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 385	3.3	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 389	3.6	5.37	Pi/Cation	false
O4	O2'	FAD- 400	2.6	154.89	H-Bond (Protein Donor)	false
O5A	O	HOH- 440	2.71	166.89	H-Bond (Protein Donor)	false