scPDB - 1mc5 entry

Protein Data Bank Entry:

PDB ID : 1mc5

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2002-08-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alcohol dehydrogenase class-3
ID:	ADHX_HUMAN
AC:	P11766
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	89 %
B	11 %

Ligand binding site composition:

B-Factor:	41.317
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:	NAD
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.003	806.625

% Hydrophobic	% Polar
57.74	42.26
According to VolSite

Ligand :

HET Code:	AHE
Formula:	C11H18N3O7S
Molecular weight:	336.342 g/mol
DrugBank ID:	DB04153
Buried Surface Area:	62.2 %
Polar Surface area:	211.63 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
52.8313	23.6039	1.32836

Binding mode :

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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
SG2	CG2	THR- 46	4.06	0	Hydrophobic	false
CD2	CB	THR- 46	4.26	0	Hydrophobic	false
OE2	OG1	THR- 46	2.51	141.82	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 55	3.07	164.01	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 57	3.15	137.97	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 57	3.15	0	Ionic (Ligand Cationic)	false
CB2	CE2	TYR- 92	3.76	0	Hydrophobic	false
CD2	CZ	TYR- 92	3.95	0	Hydrophobic	false
O31	CZ	ARG- 114	3.73	0	Ionic (Protein Cationic)	false
O32	CZ	ARG- 114	3.37	0	Ionic (Protein Cationic)	false
O31	NH2	ARG- 114	2.89	168.83	H-Bond (Protein Donor)	false
O32	NE	ARG- 114	2.67	152.71	H-Bond (Protein Donor)	false
O32	NH2	ARG- 114	3.25	127.08	H-Bond (Protein Donor)	false
CB2	CE	MET- 140	4.38	0	Hydrophobic	false
CD2	CE	MET- 140	4.31	0	Hydrophobic	false
CD2	SG	CYS- 173	3.51	0	Hydrophobic	false
SG2	CG2	VAL- 293	3.64	0	Hydrophobic	false
CG1	CG1	VAL- 293	3.57	0	Hydrophobic	false
CB1	CD1	PHE- 305	3.88	0	Hydrophobic	false
OE2	ZN	ZN- 376	2.08	0	Metal Acceptor	false
CD2	C3N	NAD- 500	3.35	0	Hydrophobic	false
SG2	C3N	NAD- 500	3.48	0	Hydrophobic	false