scPDB - 4z0p entry

Protein Data Bank Entry:

PDB ID : 4z0p

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2015-03-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent dehydrogenase
ID:	Q92T34_RHIME
AC:	Q92T34
Organism:	Rhizobium meliloti
Reign:	Bacteria
TaxID:	266834
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.735
Number of residues:	51
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.412	658.125

% Hydrophobic	% Polar
42.56	57.44
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	69.69 %
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
38.2648	-23.885	-15.8259

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	ALA- 74	4.49	0	Hydrophobic	false
C5N	CB	ALA- 74	3.94	0	Hydrophobic	false
O1A	CZ	ARG- 92	3.9	0	Ionic (Protein Cationic)	false
O2N	CZ	ARG- 92	3.46	0	Ionic (Protein Cationic)	false
O2N	NH1	ARG- 92	2.82	159.23	H-Bond (Protein Donor)	false
O2N	NH2	ARG- 92	3.21	137.01	H-Bond (Protein Donor)	false
C5N	CD2	LEU- 98	4.33	0	Hydrophobic	false
C3N	CE	MET- 102	3.53	0	Hydrophobic	false
O3B	N	MET- 147	3.04	134.24	H-Bond (Protein Donor)	false
O2A	N	VAL- 149	2.91	168.63	H-Bond (Protein Donor)	false
O1N	N	LEU- 150	2.93	167.95	H-Bond (Protein Donor)	false
C5D	CD1	LEU- 150	4.19	0	Hydrophobic	false
C5N	CD1	LEU- 150	3.75	0	Hydrophobic	false
C1B	CB	SER- 169	4.27	0	Hydrophobic	false
O2X	OG	SER- 171	2.8	149.13	H-Bond (Protein Donor)	false
O2X	N	SER- 171	3.19	164.4	H-Bond (Protein Donor)	false
O1X	NH1	ARG- 173	2.76	122.83	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 173	3.3	0	Ionic (Protein Cationic)	false
C1B	CD2	LEU- 200	3.81	0	Hydrophobic	false
C5B	CG	PRO- 201	4.14	0	Hydrophobic	false
N7N	O	ALA- 232	2.94	149.44	H-Bond (Ligand Donor)	false
N7N	OD2	ASP- 258	2.91	172.32	H-Bond (Ligand Donor)	false
O7N	N	ALA- 285	3.17	163.21	H-Bond (Protein Donor)	false
C4N	CB	ALA- 285	3.91	0	Hydrophobic	false
C5B	CD2	TYR- 319	4.36	0	Hydrophobic	false
C2B	CE2	TYR- 319	3.91	0	Hydrophobic	false
O3X	OH	TYR- 319	2.81	168.92	H-Bond (Protein Donor)	false
O1N	O	HOH- 574	2.71	179.95	H-Bond (Protein Donor)	false