Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
24.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.46, Jaccard 0.32
Reason: no major geometry red flags detected
2 protein-contact clashes
74% of hydrophobic surface is solvent-exposed (20/27 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
vB — Very bioaccumulative (BCF>5000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.603 kcal/mol/HA)
✓ Good fit quality (FQ -5.99)
✓ Strong H-bond network (6 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (24.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (10)
✗ Many internal clashes (15)
Score
-19.906
kcal/mol
LE
-0.603
kcal/mol/HA
Fit Quality
-5.99
FQ (Leeson)
HAC
33
heavy atoms
MW
451
Da
LogP
6.36
cLogP
Final rank
2.5752
rank score
Inter norm
-0.730
normalised
Contacts
12
H-bonds 7
Interaction summary
HBD 1
HBA 5
HY 4
PI 0
CLASH 2
Interaction summary
HBD 1
HBA 5
HY 4
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | 9IFF | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA209
ARG74
ASN208
GLY214
GLY215
GLY85
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
| Current overlap | 6 | Native recall | 0.46 |
| Jaccard | 0.32 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
489 residues
| Protein target | T15 | Atoms | 7420 |
|---|---|---|---|
| Residues | 489 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 634 | 0.7703295841755433 | -1.01228 | -30.485 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 619 | 0.9227104539675254 | -0.988832 | -29.8563 | 3 | 18 | 0 | 0.00 | - | - | no | Open |
| 635 | 0.9872537622581262 | -0.909874 | -26.5051 | 1 | 17 | 0 | 0.00 | - | - | no | Open |
| 624 | 1.3874062123717454 | -0.912299 | -28.609 | 1 | 18 | 0 | 0.00 | - | - | no | Open |
| 623 | 2.5042832255124376 | -0.78944 | -24.6851 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 641 | 2.575160669811322 | -0.729551 | -19.9056 | 7 | 12 | 6 | 0.46 | - | - | no | Current |
| 624 | 3.143187244987514 | -0.689014 | -19.0993 | 3 | 12 | 0 | 0.00 | - | - | no | Open |
| 637 | 3.1469015228773753 | -0.653269 | -16.8113 | 4 | 9 | 0 | 0.00 | - | - | no | Open |
| 623 | 3.788589440580992 | -0.75815 | -19.7132 | 1 | 18 | 0 | 0.00 | - | - | no | Open |
| 633 | 4.551784139291988 | -0.853444 | -26.9236 | 7 | 19 | 0 | 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
-19.906kcal/mol
Ligand efficiency (LE)
-0.6032kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.985
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
450.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.36
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
137.98kcal/mol
Minimised FF energy
113.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
738.5Ų
Total solvent-accessible surface area of free ligand
BSA total
457.8Ų
Buried surface area upon binding
BSA apolar
381.8Ų
Hydrophobic contacts buried
BSA polar
76.0Ų
Polar contacts buried
Fraction buried
62.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3089.5Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1565.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)