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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
42.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.56
Reason: strain 42.3 kcal/mol
strain ΔE 42.3 kcal/mol
2 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.746 kcal/mol/HA)
✓ Good fit quality (FQ -6.87)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Extreme strain energy (42.3 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (8)
✗ Internal clashes (7)
Score
-19.387
kcal/mol
LE
-0.746
kcal/mol/HA
Fit Quality
-6.87
FQ (Leeson)
HAC
26
heavy atoms
MW
434
Da
LogP
3.90
cLogP
Final rank
1.1577
rank score
Inter norm
-0.987
normalised
Contacts
15
H-bonds 11
Interaction summary
HBD 1
HBA 7
HY 2
PI 4
CLASH 2
Interaction summary
HBD 1
HBA 7
HY 2
PI 4
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
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 | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 13 | Native recall | 0.93 |
| Jaccard | 0.81 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 6 | HB residue recall | 0.75 |
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 348 | 0.8740691109670798 | -0.941479 | -19.4368 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 399 | 1.1577229792848076 | -0.986813 | -19.3868 | 11 | 15 | 13 | 0.93 | 0.56 | - | no | Current |
| 362 | 1.8207036733733963 | -1.05976 | -19.1339 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 494 | 2.004621134921909 | -0.964958 | -17.5011 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 367 | 3.0861066535632085 | -1.21974 | -29.9558 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 3.394597286173792 | -0.938909 | -18.0178 | 4 | 12 | 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
-19.387kcal/mol
Ligand efficiency (LE)
-0.7456kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.870
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
434.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.90
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
42.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.26kcal/mol
Minimised FF energy
70.96kcal/mol
SASA & burial
✓ computed
SASA (unbound)
641.2Ų
Total solvent-accessible surface area of free ligand
BSA total
453.6Ų
Buried surface area upon binding
BSA apolar
338.9Ų
Hydrophobic contacts buried
BSA polar
114.6Ų
Polar contacts buried
Fraction buried
70.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2185.4Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
793.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)