scPDB - 4ejm entry

Protein Data Bank Entry:

PDB ID : 4ejm

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2012-04-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative zinc-binding dehydrogenase
ID:	Q92PZ3_RHIME
AC:	Q92PZ3
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:	40.482
Number of residues:	53
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.291	948.375

% Hydrophobic	% Polar
46.26	53.74
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	55.67 %
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
44.4901	21.7521	16.8786

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
C4N	CB	CYS- 147	3.96	0	Hydrophobic	false
O2N	N	ILE- 171	3.14	170.88	H-Bond (Protein Donor)	false
C5D	CG1	ILE- 171	4.1	0	Hydrophobic	false
C5N	CD1	ILE- 171	3.98	0	Hydrophobic	false
O1X	OG1	THR- 191	3.4	124.14	H-Bond (Protein Donor)	false
O2X	OG1	THR- 191	2.72	151.4	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 192	3.46	127.65	H-Bond (Protein Donor)	false
O1X	NE	ARG- 192	2.74	164.43	H-Bond (Protein Donor)	false
O1X	N	ARG- 192	3.03	163.84	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 192	3.12	146.73	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 192	3.53	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 192	3.84	0	Ionic (Protein Cationic)	false
O2X	N	GLN- 193	2.91	155.31	H-Bond (Protein Donor)	false
O3X	NE2	GLN- 193	3.01	164.46	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 196	2.81	127.2	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 196	3.15	157.66	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 196	3.85	0	Ionic (Protein Cationic)	false
C1B	CB	ALA- 238	4.46	0	Hydrophobic	false
N6A	OE2	GLU- 242	3.36	147.58	H-Bond (Ligand Donor)	false
N7N	O	LEU- 260	3.07	172.74	H-Bond (Ligand Donor)	false
O3D	N	VAL- 262	2.88	159.55	H-Bond (Protein Donor)	false
C2D	CG2	VAL- 262	4.39	0	Hydrophobic	false
N7N	O	SER- 286	2.88	156.59	H-Bond (Ligand Donor)	false
O7N	N	ILE- 288	2.86	140.26	H-Bond (Protein Donor)	false
O1A	O	HOH- 528	2.74	152.81	H-Bond (Protein Donor)	false
O2N	O	HOH- 583	2.67	179.97	H-Bond (Protein Donor)	false