scPDB - 4dmm entry

Protein Data Bank Entry:

PDB ID : 4dmm

Resolution :2.380 Å

Experimental Method : X-ray

Deposition Date : 2012-02-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-oxoacyl-[acyl-carrier-protein] reductase
ID:	Q31QF3_SYNE7
AC:	Q31QF3
Organism:	Synechococcus elongatus
Reign:	Bacteria
TaxID:	1140
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.520
Number of residues:	45
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.816	769.500

% Hydrophobic	% Polar
34.65	65.35
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	68.29 %
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
8.58952	43.1146	50.8333

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	SER- 17	3.34	146.19	H-Bond (Protein Donor)	false
O1X	OG	SER- 17	3.07	148.51	H-Bond (Protein Donor)	false
O3B	OG	SER- 17	2.96	161.78	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 18	3.98	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 18	3.69	0	Ionic (Protein Cationic)	false
O1X	CZ	ARG- 18	4	0	Ionic (Protein Cationic)	false
O2N	N	ILE- 20	2.7	164.19	H-Bond (Protein Donor)	false
C5D	CB	ILE- 20	3.91	0	Hydrophobic	false
C4D	CD1	ILE- 20	4.38	0	Hydrophobic	false
C3N	CD1	ILE- 20	4.16	0	Hydrophobic	false
O2X	N	ALA- 40	2.94	162.65	H-Bond (Protein Donor)	false
O2X	N	SER- 41	2.77	169.25	H-Bond (Protein Donor)	false
O3X	OG	SER- 41	3.37	137.3	H-Bond (Protein Donor)	false
O2X	N	SER- 42	2.82	170.66	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 66	2.78	175.53	H-Bond (Ligand Donor)	false
N1A	N	VAL- 67	3.01	151.93	H-Bond (Protein Donor)	false
C1B	CB	ALA- 94	4.28	0	Hydrophobic	false
C4D	CG2	ILE- 143	3.97	0	Hydrophobic	false
C5N	CB	SER- 145	3.4	0	Hydrophobic	false
C2D	CZ	TYR- 158	4.4	0	Hydrophobic	false
O3D	NZ	LYS- 162	2.79	155.64	H-Bond (Protein Donor)	false
C5N	CB	PRO- 188	3.74	0	Hydrophobic	false
O7N	N	ILE- 191	2.97	163.99	H-Bond (Protein Donor)	false
O1N	OG1	THR- 193	2.74	131.74	H-Bond (Protein Donor)	false