scPDB - 2d4e entry

Protein Data Bank Entry:

PDB ID : 2d4e

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2005-10-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenaseiheyensis HTE831]
ID:	Q5SJP9_THET8
AC:	Q5SJP9
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.603
Number of residues:	56
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
1.112	594.000

% Hydrophobic	% Polar
59.09	40.91
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	71.21 %
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
-29.7759	-15.6129	-0.250182

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
C1B	CG2	ILE- 169	3.53	0	Hydrophobic	false
O3B	O	THR- 170	2.6	165.37	H-Bond (Ligand Donor)	false
C5D	CB	PRO- 171	4.22	0	Hydrophobic	false
C5N	CG	PRO- 171	4.04	0	Hydrophobic	false
C4N	CD2	LEU- 178	4.21	0	Hydrophobic	false
C5N	CD1	LEU- 178	3.55	0	Hydrophobic	false
O2B	NZ	LYS- 196	2.71	149.43	H-Bond (Protein Donor)	false
C3B	CB	ALA- 198	4.16	0	Hydrophobic	false
O2B	OE2	GLU- 199	2.84	151.52	H-Bond (Ligand Donor)	false
C4B	CD1	LEU- 247	4.27	0	Hydrophobic	false
C4N	CG2	THR- 248	3.36	0	Hydrophobic	false
O2A	N	GLU- 250	3.1	162.24	H-Bond (Protein Donor)	false
C4D	CG	GLU- 250	3.98	0	Hydrophobic	false
O2A	OG1	THR- 253	2.78	154.07	H-Bond (Protein Donor)	false
C1B	CG2	THR- 253	4.46	0	Hydrophobic	false
C3N	CB	GLU- 271	4.37	0	Hydrophobic	false
N7N	O	LEU- 272	3.08	168.38	H-Bond (Ligand Donor)	false
C2D	CB	CYS- 305	3.82	0	Hydrophobic	false
C5N	CB	CYS- 305	3.84	0	Hydrophobic	false
C4N	SG	CYS- 305	3.22	0	Hydrophobic	false
O3D	OE1	GLU- 409	3.44	149.22	H-Bond (Ligand Donor)	false
O3D	OE2	GLU- 409	2.52	151.89	H-Bond (Ligand Donor)	false
C5D	CE2	PHE- 411	3.83	0	Hydrophobic	false
C4D	CZ	PHE- 411	4.47	0	Hydrophobic	false
C2D	CE1	PHE- 411	3.48	0	Hydrophobic	false