scPDB - 2bbw entry

Protein Data Bank Entry:

PDB ID : 2bbw

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2005-10-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylate kinase 4, mitochondrial
ID:	KAD4_HUMAN
AC:	P27144
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	41.101
Number of residues:	55
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.315	766.125

% Hydrophobic	% Polar
34.80	65.20
According to VolSite

Ligand :

HET Code:	GP5
Formula:	C20H24N10O24P5
Molecular weight:	943.326 g/mol
DrugBank ID:	-
Buried Surface Area:	56.66 %
Polar Surface area:	575.05 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	8
Rings:	6
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
20.1752	-0.287407	-5.05537

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
OAI	N	GLY- 15	3.23	130.5	H-Bond (Protein Donor)	false
OAH	N	GLY- 17	3.41	145.2	H-Bond (Protein Donor)	false
OBH	N	GLY- 17	3.05	126.04	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 18	2.62	164.23	H-Bond (Protein Donor)	false
OAH	NZ	LYS- 18	2.63	175.25	H-Bond (Protein Donor)	false
OAH	N	LYS- 18	3.44	142.64	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 18	2.62	0	Ionic (Protein Cationic)	false
OAH	NZ	LYS- 18	2.63	0	Ionic (Protein Cationic)	false
OAQ	N	GLY- 19	2.82	141.13	H-Bond (Protein Donor)	false
OAO	OG1	THR- 20	2.57	167.25	H-Bond (Protein Donor)	false
OAO	N	THR- 20	2.81	159.54	H-Bond (Protein Donor)	false
O6	N	VAL- 64	3.17	139.69	H-Bond (Protein Donor)	false
N1	O	VAL- 64	2.52	152.42	H-Bond (Ligand Donor)	false
N2	O	VAL- 64	3.11	129.05	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 66	2.72	144.02	H-Bond (Ligand Donor)	false
O3'	O	GLY- 89	3.05	144.97	H-Bond (Ligand Donor)	false
C2'	CD	ARG- 92	3.43	0	Hydrophobic	false
CXB	CD	ARG- 122	4.26	0	Hydrophobic	false
DuAr	CZ	ARG- 122	3.99	22.84	Pi/Cation	false
CAV	CD2	LEU- 123	4.48	0	Hydrophobic	false
CBZ	CD	ARG- 126	4.32	0	Hydrophobic	false
CBV	CG	ARG- 126	4.32	0	Hydrophobic	false
CBV	CG1	VAL- 135	3.75	0	Hydrophobic	false
OAL	O	TYR- 136	3.17	120.47	H-Bond (Ligand Donor)	false
OAL	ND2	ASN- 137	3.21	160.42	H-Bond (Protein Donor)	false
CXB	CB	ASN- 137	4.02	0	Hydrophobic	false
NAB	OD2	ASP- 139	3.35	125.06	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 140	3.76	0	Aromatic Face/Face	false
CBW	CD1	PHE- 140	4.17	0	Hydrophobic	false
OAE	CZ	ARG- 170	3.57	0	Ionic (Protein Cationic)	false
OAE	NH1	ARG- 170	2.72	166.17	H-Bond (Protein Donor)	false
NAX	OG1	THR- 199	2.8	166.79	H-Bond (Protein Donor)	false
OAD	N	THR- 199	2.76	157.04	H-Bond (Protein Donor)	false
OAD	O	HOH- 232	2.67	139.76	H-Bond (Protein Donor)	false
OAI	O	HOH- 265	2.83	131.1	H-Bond (Protein Donor)	false