scPDB - 3utd entry

Protein Data Bank Entry:

PDB ID : 3utd

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-11-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-hydroxy-3-methylbut-2-enyl diphosphate reductase
ID:	ISPH_ECOLI
AC:	P62623
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.366
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.882	266.625

% Hydrophobic	% Polar
51.90	48.10
According to VolSite

Ligand :

HET Code:	0CJ
Formula:	C5H9O8P2
Molecular weight:	259.068 g/mol
DrugBank ID:	-
Buried Surface Area:	80.51 %
Polar Surface area:	158.47 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-38.4052	-0.365067	15.8377

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
C28	CG2	VAL- 15	3.32	0	Hydrophobic	false
O15	N	HIS- 41	2.76	176.29	H-Bond (Protein Donor)	false
O19	ND1	HIS- 41	2.83	163.12	H-Bond (Protein Donor)	false
C27	CB	ALA- 73	4.26	0	Hydrophobic	false
O15	NE2	HIS- 74	2.91	151.68	H-Bond (Protein Donor)	false
O16	NE2	HIS- 74	3.3	123.98	H-Bond (Protein Donor)	false
C22	CB	CYS- 96	4.45	0	Hydrophobic	false
C22	CG2	VAL- 99	3.42	0	Hydrophobic	false
O19	NE2	HIS- 124	2.93	167.14	H-Bond (Protein Donor)	false
C30	CG2	THR- 168	3.56	0	Hydrophobic	false
O18	OG1	THR- 168	2.84	158.92	H-Bond (Protein Donor)	false
O14	OG	SER- 225	2.64	145.14	H-Bond (Protein Donor)	false
O19	N	SER- 226	2.63	156.7	H-Bond (Protein Donor)	false
O20	N	ASN- 227	2.72	167.26	H-Bond (Protein Donor)	false
O20	ND2	ASN- 227	2.83	154.78	H-Bond (Protein Donor)	false
C28	CB	SER- 269	4.3	0	Hydrophobic	false
O14	OG	SER- 269	2.72	156.93	H-Bond (Protein Donor)	false