scPDB - 1m76 entry

Protein Data Bank Entry:

PDB ID : 1m76

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2002-07-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
ID:	HCDH_HUMAN
AC:	Q16836
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.35

Chains:

Chain Name:	Percentage of Residues within binding site
A	11 %
B	89 %

Ligand binding site composition:

B-Factor:	17.835
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.154	658.125

% Hydrophobic	% Polar
47.18	52.82
According to VolSite

Ligand :

HET Code:	CAA
Formula:	C25H36N7O18P3S
Molecular weight:	847.576 g/mol
DrugBank ID:	DB03059
Buried Surface Area:	47.32 %
Polar Surface area:	446.75 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
16.3085	6.75107	-38.8674

Binding mode :

What is Poseview ?

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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
O7A	NZ	LYS- 68	3.74	0	Ionic (Protein Cationic)	false
C3B	CD	LYS- 68	3.66	0	Hydrophobic	false
C2	SG	CYS- 137	4.3	0	Hydrophobic	false
C4	SG	CYS- 137	3.38	0	Hydrophobic	false
S1P	CD2	PHE- 160	4.3	0	Hydrophobic	false
C2	CD2	PHE- 160	3.64	0	Hydrophobic	false
N4P	O	ASN- 161	2.66	176.23	H-Bond (Ligand Donor)	false
O1	N	ASN- 161	2.95	178.39	H-Bond (Protein Donor)	false
CDP	CG	PRO- 162	4	0	Hydrophobic	false
CEP	CG	PRO- 162	4.28	0	Hydrophobic	false
C1B	CG2	VAL- 165	4	0	Hydrophobic	false
CDP	CG1	VAL- 165	3.84	0	Hydrophobic	false
CDP	SD	MET- 166	3.76	0	Hydrophobic	false
C6P	CE	MET- 166	4.11	0	Hydrophobic	false
S1P	CD2	LEU- 211	3.46	0	Hydrophobic	false
CAP	CB	PRO- 243	3.86	0	Hydrophobic	false
CEP	CE	MET- 244	4.16	0	Hydrophobic	false
C6P	SD	MET- 244	4.31	0	Hydrophobic	false
C6P	CD1	LEU- 249	3.83	0	Hydrophobic	false
C2P	CD1	LEU- 249	4.11	0	Hydrophobic	false
CEP	CZ	TYR- 252	3.87	0	Hydrophobic	false
C2P	CG2	VAL- 253	3.92	0	Hydrophobic	false
C4	CG1	VAL- 253	4.34	0	Hydrophobic	false
C2	C4N	NAD- 750	3.52	0	Hydrophobic	false
C4	C4N	NAD- 750	3.9	0	Hydrophobic	false