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. Author manuscript; available in PMC: 2018 Jan 22.
Published in final edited form as: J Chem Inf Model. 2016 Nov 18;56(12):2388–2400. doi: 10.1021/acs.jcim.6b00362

Table 1.

Comparison of Receptor Models Used for FEP+ Calculationsa

target input
protein
structure
for FEP+		 resolution (Å) whole
protein
identity
(%)		 binding
site
identity
(%)		 binding site
RMSD (Å)
backbone/side
chains
T4 lysozyme L99A 181l 1.80
184l 1.80 100 100 0.29/0.42
2oty 1.83 100 100 1.62/2.00
BRD4 3mxf 1.60
hm-3s91 (BRD3) 2.06 80 91 1.65/1.83
hm-3oni (BRD2) 1.61 38 60 1.68/1.69
MCL-1 human 4hw3 2.40
hm-2nl9 (MCL-1 rat) 1.55 87 63 2.11/2.67
hm-4lvt (Bcl-xL) 2.05 22 35 2.67/3.28
Tyk2 4gih 2.00
hm-3eyg (JAK1) 1.90 58 79 0.89/1.57
hm-3eqr (ACK1) 2.00 38 36 1.11/2.04
hm-1byg (CSK) 2.40 31 21 1.84/3.28
3nyx 2.50 100 100 2.61/3.03
A2A 4eiy 1.80 100
hm-4amj (β1-AR) 2.30 28 28 5.79/7.38
a

The second column either shows the PDB code of the crystal structure or the PDB structure used as template for building a homology model (with prefix “hm”). The target name is specified in parentheses if not identical to the original target. The “binding site” is defined as all residues within 5 Å of the cocrystallized ligand. Identity and RMSD measurements are relative to the first structure listed for each target.