scPDB - 1m9h entry

Protein Data Bank Entry:

PDB ID : 1m9h

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2002-07-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2,5-diketo-D-gluconic acid reductase A
ID:	DKGA_CORSC
AC:	P06632
Organism:	Corynebacterium sp.
Reign:	Bacteria
TaxID:	268952
EC Number:	1.1.1.346

Chains:

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

Ligand binding site composition:

B-Factor:	24.263
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.696	459.000

% Hydrophobic	% Polar
48.53	51.47
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	69.28 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
36.1575	14.2767	5.14807

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
C3D	CB	TYR- 22	3.23	0	Hydrophobic	false
C2D	CG	TYR- 22	3.98	0	Hydrophobic	false
O3D	N	TYR- 22	3.32	144.19	H-Bond (Protein Donor)	false
O2D	OD1	ASP- 45	2.85	154.47	H-Bond (Ligand Donor)	false
C2D	CZ	TYR- 50	4.26	0	Hydrophobic	false
N7N	OG	SER- 139	2.83	154.85	H-Bond (Ligand Donor)	false
O7N	ND2	ASN- 140	3.15	162.29	H-Bond (Protein Donor)	false
N7N	OE1	GLN- 161	2.98	162.36	H-Bond (Ligand Donor)	false
C4N	CD2	TRP- 187	3	0	Hydrophobic	false
C3N	CB	TRP- 187	3.71	0	Hydrophobic	false
O5D	N	GLY- 188	3.07	136.65	H-Bond (Protein Donor)	false
C5D	CG	PRO- 189	4.44	0	Hydrophobic	false
O1A	N	LEU- 190	2.7	137.28	H-Bond (Protein Donor)	false
O1A	N	GLN- 192	3.02	153.96	H-Bond (Protein Donor)	false
O1N	NE2	GLN- 192	3.08	159.91	H-Bond (Protein Donor)	false
C4D	CD2	PHE- 230	3.77	0	Hydrophobic	false
O2A	N	GLY- 232	3.38	163.13	H-Bond (Protein Donor)	false
C2B	CB	SER- 233	4.35	0	Hydrophobic	false
DuAr	DuAr	HIS- 238	3.62	0	Aromatic Face/Face	false
N6A	OE2	GLU- 241	3.18	165.78	H-Bond (Ligand Donor)	false
N7A	ND2	ASN- 242	2.79	170.34	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 242	2.93	148.89	H-Bond (Ligand Donor)	false