scPDB - 3pdu entry

Protein Data Bank Entry:

PDB ID : 3pdu

Resolution :1.890 Å

Experimental Method : X-ray

Deposition Date : 2010-10-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase
ID:	Q74DE4_GEOSL
AC:	Q74DE4
Organism:	Geobacter sulfurreducens
Reign:	Bacteria
TaxID:	243231
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.933
Number of residues:	52
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.800	1680.750

% Hydrophobic	% Polar
44.18	55.82
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	72 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-49.9354	35.8506	-33.0577

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
O2A	N	ILE- 11	2.87	178.26	H-Bond (Protein Donor)	false
O2N	N	MET- 12	2.81	168.18	H-Bond (Protein Donor)	false
C3N	CG	MET- 12	3.49	0	Hydrophobic	false
C4N	CE	MET- 12	3.47	0	Hydrophobic	false
O3B	OD1	ASN- 31	2.75	120.24	H-Bond (Ligand Donor)	false
O3X	ND2	ASN- 31	2.75	173.43	H-Bond (Protein Donor)	false
O1X	NE	ARG- 32	2.96	173.16	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 32	3.04	172.85	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 32	3.77	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 32	3.95	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 32	3.94	151.84	Pi/Cation	false
O1X	N	ASN- 33	3.03	136.5	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 36	3.91	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 36	2.8	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 36	2.8	151.71	H-Bond (Protein Donor)	false
C5D	CG	MET- 64	4.19	0	Hydrophobic	false
C4D	SD	MET- 64	4.05	0	Hydrophobic	false
C1B	CD2	LEU- 65	4.02	0	Hydrophobic	false
O3D	O	LEU- 65	3.05	144.23	H-Bond (Ligand Donor)	false
O4B	N	ALA- 66	3.06	128	H-Bond (Protein Donor)	false
C5B	CB	ALA- 66	3.69	0	Hydrophobic	false
N6A	OE1	GLU- 73	2.9	166.09	H-Bond (Ligand Donor)	false
O3D	N	THR- 96	3.01	151.14	H-Bond (Protein Donor)	false
C2D	CB	THR- 96	4.48	0	Hydrophobic	false
C5N	CG2	VAL- 121	3.81	0	Hydrophobic	false
N7N	O	SER- 231	2.89	154.99	H-Bond (Ligand Donor)	false
C2D	CE1	PHE- 232	4.18	0	Hydrophobic	false
O1A	NE2	HIS- 236	2.9	165.74	H-Bond (Protein Donor)	false
O3	NE2	HIS- 236	3.21	122.79	H-Bond (Protein Donor)	false
C2D	CB	HIS- 236	4.37	0	Hydrophobic	false
O3D	NZ	LYS- 239	3.24	128.57	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 239	2.93	145.07	H-Bond (Protein Donor)	false
O2D	O	HOH- 296	2.73	157.04	H-Bond (Ligand Donor)	false
O2N	O	HOH- 312	2.74	154.59	H-Bond (Protein Donor)	false