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
17.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.43
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.230 kcal/mol/HA)
✓ Good fit quality (FQ -11.03)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (17.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-29.526
kcal/mol
LE
-1.230
kcal/mol/HA
Fit Quality
-11.03
FQ (Leeson)
HAC
24
heavy atoms
MW
368
Da
LogP
2.43
cLogP
Final rank
3.9843
rank score
Inter norm
-1.393
normalised
Contacts
20
H-bonds 8
Interaction summary
HBD 2
HBA 5
PC 1
HY 6
PI 1
CLASH 1
Interaction summary
HBD 2
HBA 5
PC 1
HY 6
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| HB same residue | 4 | HB residue recall | 0.57 |
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 663 | 1.8318066994046442 | -1.12484 | -23.824 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 654 | 2.6135148345167436 | -1.15722 | -26.2556 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 654 | 3.1427476690832297 | -1.13387 | -23.6503 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 3.186904029274852 | -1.05913 | -24.8813 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 657 | 3.9843393634997644 | -1.39289 | -29.5256 | 8 | 20 | 15 | 0.79 | 0.43 | - | no | Current |
| 659 | 5.110545450686871 | -1.20698 | -24.3241 | 10 | 16 | 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
-29.526kcal/mol
Ligand efficiency (LE)
-1.2302kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.025
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
368.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.43
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-105.29kcal/mol
Minimised FF energy
-123.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
604.6Ų
Total solvent-accessible surface area of free ligand
BSA total
501.8Ų
Buried surface area upon binding
BSA apolar
326.1Ų
Hydrophobic contacts buried
BSA polar
175.7Ų
Polar contacts buried
Fraction buried
83.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2513.8Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1376.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)