scPDB - 4zz7 entry

Protein Data Bank Entry:

PDB ID : 4zz7

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2015-05-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methylmalonate-semialdehyde dehydrogenase
ID:	G5CZI2_9GAMM
AC:	G5CZI2
Organism:	Oceanimonas doudoroffii
Reign:	Bacteria
TaxID:	84158
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.115
Number of residues:	51
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.519	779.625

% Hydrophobic	% Polar
45.45	54.55
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	71.77 %
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
130.121	22.1133	29.5833

Binding mode :

What is Poseview ?

2D View
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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
C4B	CG2	ILE- 145	3.86	0	Hydrophobic	false
O3B	O	THR- 146	3.12	164.96	H-Bond (Ligand Donor)	false
C5B	CB	PRO- 147	4.14	0	Hydrophobic	false
C5D	CB	PRO- 147	4.12	0	Hydrophobic	false
O1N	N	PHE- 148	3.24	126.67	H-Bond (Protein Donor)	false
C5D	CE2	PHE- 148	3.52	0	Hydrophobic	false
O3B	NZ	LYS- 172	2.68	139.05	H-Bond (Protein Donor)	false
O2B	OE2	GLU- 175	3.11	150.94	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 175	2.85	143.42	H-Bond (Ligand Donor)	false
N1A	NZ	LYS- 205	3.49	169.1	H-Bond (Protein Donor)	false
C4B	CE1	PHE- 222	3.86	0	Hydrophobic	false
C3N	CG1	VAL- 223	3.51	0	Hydrophobic	false
O2A	OG	SER- 225	2.68	141.8	H-Bond (Protein Donor)	false
O2A	N	SER- 225	2.64	152.6	H-Bond (Protein Donor)	false
C3D	CB	SER- 225	4.48	0	Hydrophobic	false
C3N	SG	CYS- 280	3.55	0	Hydrophobic	false
O3D	OE2	GLU- 382	3.48	168.87	H-Bond (Ligand Donor)	false
O2D	OE2	GLU- 382	3.35	168.76	H-Bond (Ligand Donor)	false
C5D	CE2	PHE- 384	4.01	0	Hydrophobic	false
C2D	CE1	PHE- 384	3.56	0	Hydrophobic	false
C3D	CZ	PHE- 384	3.64	0	Hydrophobic	false