scPDB - 4pmj entry

Protein Data Bank Entry:

PDB ID : 4pmj

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2014-05-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative oxidoreductase
ID:	Q92NR7_RHIME
AC:	Q92NR7
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:	25.027
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.476	634.500

% Hydrophobic	% Polar
47.87	52.13
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	71.24 %
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
1.966	-5.93702	10.0813

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
O2D	N	THR- 23	3.42	162.85	H-Bond (Protein Donor)	false
O3D	N	TRP- 24	2.94	141.9	H-Bond (Protein Donor)	false
C3D	CB	TRP- 24	3.51	0	Hydrophobic	false
O2D	OD2	ASP- 52	2.71	140.17	H-Bond (Ligand Donor)	false
C2D	CE2	TYR- 57	3.98	0	Hydrophobic	false
N7N	OG	SER- 144	2.87	135.63	H-Bond (Ligand Donor)	false
O7N	ND2	ASN- 145	3.06	153.13	H-Bond (Protein Donor)	false
N7N	OE1	GLN- 167	2.99	171.13	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 195	3.63	0	Aromatic Face/Face	false
C5N	CB	TYR- 195	4.06	0	Hydrophobic	false
O2N	OG	SER- 196	2.73	147.31	H-Bond (Protein Donor)	false
O5D	N	SER- 196	3.07	122.07	H-Bond (Protein Donor)	false
O5D	OG	SER- 196	3.35	121.14	H-Bond (Protein Donor)	false
O2A	N	LEU- 198	2.74	144.19	H-Bond (Protein Donor)	false
C1B	CD1	LEU- 198	4.44	0	Hydrophobic	false
O2A	N	GLU- 200	3.14	146.53	H-Bond (Protein Donor)	false
C4D	CD1	ILE- 237	4.15	0	Hydrophobic	false
O1A	N	LYS- 239	2.95	161.05	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 239	2.7	177.92	H-Bond (Protein Donor)	false
C3B	CD	LYS- 239	4.25	0	Hydrophobic	false
C5D	CB	LYS- 239	4.08	0	Hydrophobic	false
O1X	NZ	LYS- 239	2.7	0	Ionic (Protein Cationic)	false
O3X	OG1	THR- 240	2.56	158.35	H-Bond (Protein Donor)	false
O1X	N	GLY- 241	2.79	164.82	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 245	2.58	163.59	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 245	3.57	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 245	3.98	148.99	Pi/Cation	false
N6A	OE2	GLU- 248	2.81	170.83	H-Bond (Ligand Donor)	false
N7A	ND2	ASN- 249	3.41	156.13	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 249	2.82	162.16	H-Bond (Ligand Donor)	false