scPDB - 3wbf entry

Protein Data Bank Entry:

PDB ID : 3wbf

Resolution :2.120 Å

Experimental Method : X-ray

Deposition Date : 2013-05-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Meso-diaminopimelate D-dehydrogenase
ID:	Q67PI3_SYMTH
AC:	Q67PI3
Organism:	Symbiobacterium thermophilum
Reign:	Bacteria
TaxID:	292459
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.865
Number of residues:	50
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.434	583.875

% Hydrophobic	% Polar
45.66	54.34
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	69.04 %
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
10.5786	73.7959	46.834

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
O1X	N	TYR- 11	2.95	162.54	H-Bond (Protein Donor)	false
O1A	N	ASN- 13	2.97	170.25	H-Bond (Protein Donor)	false
O2N	ND2	ASN- 13	3	155.48	H-Bond (Protein Donor)	false
O1N	N	VAL- 14	2.92	163.83	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 14	4.3	0	Hydrophobic	false
O1X	NE	ARG- 35	2.92	171.01	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 35	3.79	0	Ionic (Protein Cationic)	false
O2X	NE	ARG- 36	2.9	145.36	H-Bond (Protein Donor)	false
O2X	N	ARG- 36	2.89	163.61	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 36	2.97	158.73	H-Bond (Protein Donor)	false
O3X	NE	ARG- 36	3.3	141.23	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 36	3.92	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 36	3.57	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 36	3.81	24.62	Pi/Cation	false
C1B	CG1	VAL- 68	4.33	0	Hydrophobic	false
C5B	CG	PRO- 69	4.3	0	Hydrophobic	false
O3D	N	THR- 70	3.1	161.77	H-Bond (Protein Donor)	false
O2D	OG1	THR- 70	2.62	156.23	H-Bond (Protein Donor)	false
C3N	CB	SER- 90	3.9	0	Hydrophobic	false
N7N	O	SER- 90	2.73	147.83	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 92	2.7	133.48	H-Bond (Ligand Donor)	false
O7N	N	TRP- 121	3	121.06	H-Bond (Protein Donor)	false
O7N	N	ASP- 122	3.04	167.44	H-Bond (Protein Donor)	false
C5N	CG	MET- 152	3.93	0	Hydrophobic	false
C5D	CG2	VAL- 156	4.25	0	Hydrophobic	false
C3D	CG2	VAL- 156	4.04	0	Hydrophobic	false
O1A	NZ	LYS- 159	3.91	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 159	3.07	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 159	3.07	152.48	H-Bond (Protein Donor)	false
C4N	CG2	THR- 257	3.76	0	Hydrophobic	false
C4N	C5	API- 301	3.8	0	Hydrophobic	false
O1N	O	HOH- 466	2.69	179.98	H-Bond (Protein Donor)	false