Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
12.0 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.65, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET
GDS: UNSAFE
UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.391
ADMET + ECO + DL
ADMETscore (GDS)
0.398
absorption · distr. · metab.
DLscore
0.444
drug-likeness
P(SAFE)
0.25
GDS classification
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.200 kcal/mol/HA)
✓ Good fit quality (FQ -10.91)
✓ Good H-bonds (3 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Moderate strain (12.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-29.999
kcal/mol
LE
-1.200
kcal/mol/HA
Fit Quality
-10.91
FQ (Leeson)
HAC
25
heavy atoms
MW
395
Da
LogP
3.17
cLogP
Final rank
0.8369
rank score
Inter norm
-1.224
normalised
Contacts
14
H-bonds 6
Interaction summary
HBD 1
HBA 2
HY 9
PI 4
CLASH 2
Interaction summary
HBD 1
HBA 2
HY 9
PI 4
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER207
SER95
TRP221
TYR174
TYR98
VAL206
| ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| Residue summary | LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NAP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 429 | 0.3580919713066338 | -1.10627 | -22.4548 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 369 | 0.8369236842974171 | -1.2245 | -29.9994 | 6 | 14 | 13 | 0.68 | 0.40 | - | no | Current |
| 349 | 2.44111177040875 | -1.12817 | -25.6437 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 2.596782112753742 | -0.83916 | -18.0269 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 3.432930616002931 | -1.59331 | -37.0484 | 12 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.999kcal/mol
Ligand efficiency (LE)
-1.2000kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.909
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
394.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.17
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-73.90kcal/mol
Minimised FF energy
-85.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
584.6Ų
Total solvent-accessible surface area of free ligand
BSA total
508.1Ų
Buried surface area upon binding
BSA apolar
348.4Ų
Hydrophobic contacts buried
BSA polar
159.7Ų
Polar contacts buried
Fraction buried
86.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1535.0Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
932.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)