scPDB - 4cpd entry

Protein Data Bank Entry:

PDB ID : 4cpd

Resolution :2.740 Å

Experimental Method : X-ray

Deposition Date : 2014-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alcohol dehydrogenase
ID:	B2ZRE3_9DEIN
AC:	B2ZRE3
Organism:	Thermus sp. ATN1
Reign:	Bacteria
TaxID:	528218
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
D	98 %

Ligand binding site composition:

B-Factor:	55.704
Number of residues:	52
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.344	1377.000

% Hydrophobic	% Polar
54.90	45.10
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.25 %
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
20.007	8.1585	68.7063

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
C5N	SG	CYS- 38	4.29	0	Hydrophobic	false
O1N	N	GLY- 39	3.09	126.03	H-Bond (Protein Donor)	false
O2D	OG	SER- 40	3.05	174.99	H-Bond (Protein Donor)	false
O3D	NE2	HIS- 43	3.31	170.66	H-Bond (Protein Donor)	false
O2D	NE2	HIS- 43	3.37	124.78	H-Bond (Protein Donor)	false
C4N	CG2	THR- 156	3.48	0	Hydrophobic	false
O2N	N	VAL- 180	3.12	157.72	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 180	4.22	0	Hydrophobic	false
C5N	CG2	VAL- 180	4.06	0	Hydrophobic	false
O3B	OD2	ASP- 200	3.26	162.24	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 200	3.3	141.45	H-Bond (Ligand Donor)	false
C2B	CD1	ILE- 202	4.2	0	Hydrophobic	false
O1A	NH1	ARG- 205	2.77	131.77	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 205	3.76	0	Ionic (Protein Cationic)	false
C3B	CD	ARG- 205	4.39	0	Hydrophobic	false
C1B	CG2	VAL- 244	4.27	0	Hydrophobic	false
O3D	O	VAL- 244	2.94	148.59	H-Bond (Ligand Donor)	false
N7N	O	VAL- 266	2.79	170.41	H-Bond (Ligand Donor)	false
O3D	N	VAL- 268	3.34	151.87	H-Bond (Protein Donor)	false
C2D	CG2	VAL- 268	4.36	0	Hydrophobic	false
N7N	O	GLY- 291	3.24	152.29	H-Bond (Ligand Donor)	false
O7N	N	ALA- 293	3	160.84	H-Bond (Protein Donor)	false
O2N	O	HOH- 2020	2.78	160.95	H-Bond (Protein Donor)	false
O1A	O	HOH- 2021	3.21	179.98	H-Bond (Protein Donor)	false