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
Likely artefact or unreliable pose
Binding moderate
Geometry low
Native strong
SASA done
Strain ΔE
142.4 kcal/mol
Protein clashes
0
Internal clashes
21
Native overlap
contact recall 0.93, Jaccard 0.65, H-bond role recall 0.11
Reason: 21 internal clashes, strain 142.4 kcal/mol
strain ΔE 142.4 kcal/mol
21 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good fit quality (FQ -1.67)
✓ Good H-bonds (3 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (99%)
✗ Extreme strain energy (142.4 kcal/mol)
✗ Low LE (-0.150 kcal/mol/HA)
✗ Geometry warnings
✗ Many internal clashes (21)
Score
-7.814
kcal/mol
LE
-0.150
kcal/mol/HA
Fit Quality
-1.67
FQ (Leeson)
HAC
52
heavy atoms
MW
708
Da
LogP
-3.38
cLogP
Final rank
3.8622
rank score
Inter norm
-0.464
normalised
Contacts
19
H-bonds 8
Interaction summary
HBD 1
HBA 2
HY 6
PI 3
CLASH 0
Interaction summary
HBD 1
HBA 2
HY 6
PI 3
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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
No clash · clashes detected for this pose.
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 | 0.65 | RMSD | - |
| HB strict | 2 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.11 |
| HB same residue | 1 | HB residue recall | 0.12 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 90 | 1.9758313890204 | -0.584983 | -19.702 | 1 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 106 | 2.6158617277746465 | -0.706299 | -36.6576 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 3.4428608432428507 | -0.591624 | -28.878 | 3 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 77 | 3.8621640248890254 | -0.463821 | -7.81397 | 8 | 19 | 13 | 0.93 | 0.11 | - | no | Current |
| 95 | 4.5138613769233595 | -0.515132 | -17.8071 | 3 | 25 | 0 | 0.00 | 0.00 | - | no | Open |
| 79 | 4.556755509148755 | -0.457682 | -24.6331 | 7 | 15 | 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
-7.814kcal/mol
Ligand efficiency (LE)
-0.1503kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-1.665
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
52HA
Physicochemical properties
Molecular weight
708.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-3.38
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
142.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
777.19kcal/mol
Minimised FF energy
634.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
921.7Ų
Total solvent-accessible surface area of free ligand
BSA total
548.1Ų
Buried surface area upon binding
BSA apolar
541.8Ų
Hydrophobic contacts buried
BSA polar
6.3Ų
Polar contacts buried
Fraction buried
59.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2596.7Ų
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
800.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)