scPDB - 3zhb entry

Protein Data Bank Entry:

PDB ID : 3zhb

Resolution :2.730 Å

Experimental Method : X-ray

Deposition Date : 2012-12-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative dehydrogenase
ID:	Q1EQE0_STRKN
AC:	Q1EQE0
Organism:	Streptomyces kanamyceticus
Reign:	Bacteria
TaxID:	1967
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
B	8 %

Ligand binding site composition:

B-Factor:	55.529
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.220	1542.375

% Hydrophobic	% Polar
46.17	53.83
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	52.25 %
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
-27.9012	-37.4701	19.8563

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
O3B	N	LEU- 27	3.05	137.67	H-Bond (Protein Donor)	false
O1A	N	LEU- 29	3.48	157.97	H-Bond (Protein Donor)	false
O2N	N	MET- 30	2.98	148.09	H-Bond (Protein Donor)	false
C5D	CB	MET- 30	4.34	0	Hydrophobic	false
C3N	CE	MET- 30	3.48	0	Hydrophobic	false
O3B	OD1	ASN- 49	2.66	133.57	H-Bond (Ligand Donor)	false
O2X	ND2	ASN- 49	3.12	172.81	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 50	2.6	164.48	H-Bond (Protein Donor)	false
O3X	NE	ARG- 50	3.13	166.83	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 50	3.49	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 50	3.81	167.59	Pi/Cation	false
O3X	OG1	THR- 51	3	139.96	H-Bond (Protein Donor)	false
O3X	N	THR- 51	2.84	160.85	H-Bond (Protein Donor)	false
C4D	SG	CYS- 82	3.36	0	Hydrophobic	false
C4B	CB	VAL- 83	4.38	0	Hydrophobic	false
C1B	CB	VAL- 83	4.06	0	Hydrophobic	false
O3D	O	VAL- 83	3.26	143.08	H-Bond (Ligand Donor)	false
C5B	CB	SER- 84	4.06	0	Hydrophobic	false
O3D	N	SER- 111	3.09	166.28	H-Bond (Protein Donor)	false
O2D	OG	SER- 111	2.91	158.63	H-Bond (Ligand Donor)	false
C5N	CB	ILE- 136	3.94	0	Hydrophobic	false