scPDB - 4itb entry

Protein Data Bank Entry:

PDB ID : 4itb

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2013-01-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Succinate-semialdehyde dehydrogenase
ID:	B1XMM6_SYNP2
AC:	B1XMM6
Organism:	Synechococcus sp.
Reign:	Bacteria
TaxID:	32049
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	10.271
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.291	1299.375

% Hydrophobic	% Polar
52.21	47.79
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	61.89 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
0.816625	49.7086	28.1482

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
C1B	CG1	VAL- 127	3.59	0	Hydrophobic	false
C4B	CG1	VAL- 127	3.76	0	Hydrophobic	false
O3B	O	MET- 128	2.76	164.4	H-Bond (Ligand Donor)	false
C5B	CB	PRO- 129	4.22	0	Hydrophobic	false
C4N	CB	PRO- 129	3.5	0	Hydrophobic	false
O2N	NE1	TRP- 130	2.78	161.14	H-Bond (Protein Donor)	false
O7N	ND2	ASN- 131	3.3	139.25	H-Bond (Protein Donor)	false
C4N	CB	ASN- 131	4.39	0	Hydrophobic	false
C1B	CD	LYS- 154	4.41	0	Hydrophobic	false
O1X	NZ	LYS- 154	2.78	177.68	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 154	2.78	0	Ionic (Protein Cationic)	false
C3B	CB	ALA- 156	4.05	0	Hydrophobic	false
O1X	OG	SER- 157	2.72	173.34	H-Bond (Protein Donor)	false
O3X	N	SER- 157	2.89	168.39	H-Bond (Protein Donor)	false
N7N	O	GLY- 206	3.37	147.4	H-Bond (Ligand Donor)	false
O1A	OG	SER- 207	2.57	149.71	H-Bond (Protein Donor)	false
O1A	N	SER- 207	2.8	156.38	H-Bond (Protein Donor)	false
C4D	CB	SER- 207	4	0	Hydrophobic	false
N6A	OG	SER- 213	3.2	143.07	H-Bond (Ligand Donor)	false
N7N	OE1	GLU- 228	3.1	172.33	H-Bond (Ligand Donor)	false
C5D	CD1	ILE- 309	4.28	0	Hydrophobic	false
C3D	CD1	ILE- 309	4.11	0	Hydrophobic	false
O2D	OE1	GLU- 359	2.6	175.83	H-Bond (Ligand Donor)	false
C3D	CD2	PHE- 361	3.78	0	Hydrophobic	false
C2D	CG	PHE- 361	3.54	0	Hydrophobic	false