scPDB - 3zhu entry

Protein Data Bank Entry:

PDB ID : 3zhu

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-12-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Multifunctional 2-oxoglutarate metabolism enzyme
ID:	KGD_MYCS2
AC:	A0R2B1
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	1.2.4.2

Chains:

Chain Name:	Percentage of Residues within binding site
C	29 %
D	71 %

Ligand binding site composition:

B-Factor:	29.455
Number of residues:	46
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.791	1755.000

% Hydrophobic	% Polar
39.81	60.19
According to VolSite

Ligand :

HET Code:	TD8
Formula:	C17H23N4O10P2S
Molecular weight:	537.398 g/mol
DrugBank ID:	-
Buried Surface Area:	77.49 %
Polar Surface area:	285.67 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
18.8374	14.1663	-70.872

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
C10	CZ	PHE- 506	4.06	0	Hydrophobic	false
C12	CE2	PHE- 506	3.62	0	Hydrophobic	false
O2B	NE2	HIS- 539	2.77	161.85	H-Bond (Protein Donor)	false
C12	CB	HIS- 539	3.8	0	Hydrophobic	false
O2B	CZ	ARG- 540	3.98	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 540	3.95	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 540	3.15	172.88	H-Bond (Protein Donor)	false
O3B	NE	ARG- 540	3.06	169.08	H-Bond (Protein Donor)	false
C12	CE1	TYR- 578	3.75	0	Hydrophobic	false
O11	NE2	HIS- 579	2.75	154.74	H-Bond (Protein Donor)	false
C9	CB	SER- 604	4.36	0	Hydrophobic	false
N4'	O	SER- 604	2.7	166.4	H-Bond (Ligand Donor)	false
C2A	CB	HIS- 605	4.35	0	Hydrophobic	false
N3'	N	LEU- 606	3.24	171.93	H-Bond (Protein Donor)	false
C5'	CD1	LEU- 606	4.44	0	Hydrophobic	false
C5B	CD1	LEU- 606	3.71	0	Hydrophobic	false
S1	CD1	LEU- 606	3.94	0	Hydrophobic	false
O1A	N	ALA- 646	3.04	164.74	H-Bond (Protein Donor)	false
O2A	N	ALA- 647	3.05	158.2	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 678	3.26	138.8	H-Bond (Protein Donor)	false
C5A	CB	PHE- 682	4.13	0	Hydrophobic	false
C4A	CB	GLN- 901	4.37	0	Hydrophobic	false
C2A	CD2	LEU- 950	4.44	0	Hydrophobic	false
C4A	CD1	LEU- 950	3.77	0	Hydrophobic	false
C5'	CD2	LEU- 950	4.44	0	Hydrophobic	false
C5B	CD1	LEU- 950	3.32	0	Hydrophobic	false
N1'	OE2	GLU- 952	2.62	161.69	H-Bond (Ligand Donor)	false
C35	CG	GLN- 976	3.86	0	Hydrophobic	false
C2A	CD1	PHE- 980	4.26	0	Hydrophobic	false
C35	CE2	PHE- 980	3.63	0	Hydrophobic	false
DuAr	DuAr	PHE- 980	3.66	0	Aromatic Face/Face	false
O9	NE2	HIS- 1020	3.31	165.64	H-Bond (Protein Donor)	false
O1A	MG	MG- 2002	2.25	0	Metal Acceptor	false
O1B	MG	MG- 2002	2.1	0	Metal Acceptor	false
O3B	O	HOH- 3062	2.89	140.36	H-Bond (Protein Donor)	false
O1B	O	HOH- 3082	2.63	179.94	H-Bond (Protein Donor)	false