scPDB - 4ywj entry

Protein Data Bank Entry:

PDB ID : 4ywj

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2015-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-hydroxy-tetrahydrodipicolinate reductase
ID:	DAPB_PSEAE
AC:	P38103
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.267
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.390	583.875

% Hydrophobic	% Polar
34.10	65.90
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	59.29 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
47.4288	35.1401	6.47634

Binding mode :

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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
O2A	NE	ARG- 12	3.23	149.8	H-Bond (Protein Donor)	false
O2A	N	ARG- 12	2.86	174.26	H-Bond (Protein Donor)	false
O2N	CZ	ARG- 12	3.31	0	Ionic (Protein Cationic)	false
O1N	N	MET- 13	2.88	163.12	H-Bond (Protein Donor)	false
C4N	SD	MET- 13	4.48	0	Hydrophobic	false
C5N	CG	MET- 13	3.72	0	Hydrophobic	false
O3B	OD2	ASP- 35	2.94	153.59	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 35	2.62	147.33	H-Bond (Ligand Donor)	false
C4D	CB	PHE- 76	4.28	0	Hydrophobic	false
N7N	O	GLY- 99	3.22	163.84	H-Bond (Ligand Donor)	false
O3D	N	THR- 101	3.04	172.76	H-Bond (Protein Donor)	false
O2D	OG1	THR- 101	2.66	144.82	H-Bond (Protein Donor)	false
C2D	CG2	THR- 101	4.48	0	Hydrophobic	false
N7N	O	ALA- 123	3.17	133.44	H-Bond (Ligand Donor)	false
O7N	N	PHE- 126	2.87	153.16	H-Bond (Protein Donor)	false
O2N	CZ	ARG- 237	3.88	0	Ionic (Protein Cationic)	false
O2N	NH2	ARG- 237	3.21	166.41	H-Bond (Protein Donor)	false
C4N	CB	PHE- 240	3.91	0	Hydrophobic	false
O1N	O	HOH- 431	2.64	158.76	H-Bond (Protein Donor)	false