scPDB - 1ffu entry

Protein Data Bank Entry:

PDB ID : 1ffu

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2000-07-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carbon monoxide dehydrogenase medium chain
ID:	DCMM_HYDPS
AC:	P19914
Organism:	Hydrogenophaga pseudoflava
Reign:	Bacteria
TaxID:	47421
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.621
Number of residues:	51
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.192	1154.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	73.6 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
12.4569	58.2622	117.491

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
O3B	NZ	LYS- 29	2.81	161.72	H-Bond (Protein Donor)	false
C2B	CD	LYS- 29	4.44	0	Hydrophobic	false
C2B	CB	LEU- 30	4.38	0	Hydrophobic	false
O2B	O	LEU- 30	2.83	147.84	H-Bond (Ligand Donor)	false
O1A	N	ALA- 32	2.91	156.82	H-Bond (Protein Donor)	false
C5B	CB	ALA- 32	4.47	0	Hydrophobic	false
O1P	N	GLY- 33	3.09	139.33	H-Bond (Protein Donor)	false
O3P	N	GLY- 33	3.44	125.07	H-Bond (Protein Donor)	false
O1A	N	GLY- 34	3.3	145.36	H-Bond (Protein Donor)	false
C8M	CB	HIS- 35	4.23	0	Hydrophobic	false
O2P	N	HIS- 35	3.05	142.98	H-Bond (Protein Donor)	false
O2A	N	SER- 36	3.02	139.66	H-Bond (Protein Donor)	false
O4'	OG	SER- 36	3.07	148.03	H-Bond (Protein Donor)	false
C5'	CB	SER- 36	3.34	0	Hydrophobic	false
C4'	CB	SER- 36	4.14	0	Hydrophobic	false
O2A	N	LEU- 37	2.98	169.22	H-Bond (Protein Donor)	false
O4	N	ALA- 102	3.46	170.97	H-Bond (Protein Donor)	false
C9A	CB	ALA- 102	3.94	0	Hydrophobic	false
C6	CB	ALA- 102	3.77	0	Hydrophobic	false
C8M	CG2	VAL- 106	4.32	0	Hydrophobic	false
C2'	CG1	VAL- 106	4.41	0	Hydrophobic	false
C7	CG2	VAL- 106	4.29	0	Hydrophobic	false
C9	CG1	VAL- 106	3.8	0	Hydrophobic	false
O1P	N	THR- 111	2.77	167.94	H-Bond (Protein Donor)	false
O1P	OG1	THR- 111	2.92	173.28	H-Bond (Protein Donor)	false
N1	OD2	ASP- 115	3.19	125.15	H-Bond (Protein Donor)	false
O2	OD2	ASP- 115	2.79	174.75	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 115	2.97	156.13	H-Bond (Ligand Donor)	false
C1B	CB	ALA- 117	3.75	0	Hydrophobic	false
C4B	CB	HIS- 118	4.47	0	Hydrophobic	false
C5'	CB	HIS- 118	4.42	0	Hydrophobic	false
O4'	ND2	ASN- 123	3.37	137.92	H-Bond (Protein Donor)	false
O2	N	ASP- 124	2.84	162.91	H-Bond (Protein Donor)	false
N3	OD2	ASP- 124	2.92	153.77	H-Bond (Ligand Donor)	false
N6A	O	MET- 167	2.98	159.08	H-Bond (Ligand Donor)	false
N1A	N	MET- 167	2.71	154	H-Bond (Protein Donor)	false
O4	NZ	LYS- 185	3.02	139.24	H-Bond (Protein Donor)	false
C1'	CZ2	TRP- 193	4.27	0	Hydrophobic	false
C9A	CZ2	TRP- 193	3.32	0	Hydrophobic	false