scPDB - 4jbi entry

Protein Data Bank Entry:

PDB ID : 4jbi

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2013-02-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alcohol dehydrogenase (Zinc)
ID:	Q8ZUP0_PYRAE
AC:	Q8ZUP0
Organism:	Pyrobaculum aerophilum
Reign:	Archaea
TaxID:	178306
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	89 %
D	2 %
H	9 %

Ligand binding site composition:

B-Factor:	36.315
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.785	1697.625

% Hydrophobic	% Polar
43.74	56.26
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	59.36 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-68.8415	40.4911	24.4755

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
C2D	CB	PRO- 40	4.12	0	Hydrophobic	false
O3X	CZ	ARG- 79	3.87	0	Ionic (Protein Cationic)	false
O3X	NH1	ARG- 79	2.97	131.26	H-Bond (Protein Donor)	false
C5N	CG2	ILE- 147	3.47	0	Hydrophobic	false
C4N	CG2	THR- 151	3.59	0	Hydrophobic	false
O3B	OG1	THR- 173	3.23	159.89	H-Bond (Ligand Donor)	false
O1A	N	ASN- 175	3.06	164.35	H-Bond (Protein Donor)	false
O1N	ND2	ASN- 175	2.85	159.36	H-Bond (Protein Donor)	false
O2N	N	VAL- 176	2.88	163.72	H-Bond (Protein Donor)	false
C5N	CG2	VAL- 176	3.7	0	Hydrophobic	false
O2X	OG	SER- 195	2.65	154.07	H-Bond (Protein Donor)	false
O1X	NE	ARG- 196	3.4	166.11	H-Bond (Protein Donor)	false
O1X	N	ARG- 196	2.84	162.41	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 196	2.63	149.41	H-Bond (Protein Donor)	false
O3X	NE	ARG- 196	3.1	131	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 196	3.28	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 196	3.54	163.37	Pi/Cation	false
O2X	CZ	ARG- 197	3.8	0	Ionic (Protein Cationic)	false
O2X	NE	ARG- 197	2.98	178.32	H-Bond (Protein Donor)	false
C5D	CG	PRO- 231	4.15	0	Hydrophobic	false
C4D	CB	PRO- 231	4.04	0	Hydrophobic	false
N7N	O	ALA- 253	2.85	146.22	H-Bond (Ligand Donor)	false
C5B	CD2	LEU- 256	3.86	0	Hydrophobic	false
C4D	CB	LEU- 256	4.32	0	Hydrophobic	false
C3D	CD1	LEU- 256	3.91	0	Hydrophobic	false
N7N	OG1	THR- 279	2.98	161.86	H-Bond (Ligand Donor)	false
O7N	N	GLY- 280	2.84	147.46	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 323	3.03	157.07	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 323	3.26	143.07	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 323	3.29	137.4	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 323	3.6	0	Ionic (Protein Cationic)	false
O2N	O	HOH- 517	2.72	158.63	H-Bond (Protein Donor)	false
O2D	O	HOH- 543	3.18	152.94	H-Bond (Protein Donor)	false