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 medium
Native strong
SASA done
Strain ΔE
8.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.94, Jaccard 0.84, H-bond role recall 0.73
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
53% of hydrophobic surface appears solvent-exposed (8/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.014 kcal/mol/HA)
✓ Good fit quality (FQ -8.65)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Moderate strain (8.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-21.303
kcal/mol
LE
-1.014
kcal/mol/HA
Fit Quality
-8.65
FQ (Leeson)
HAC
21
heavy atoms
MW
294
Da
LogP
3.30
cLogP
Interaction summary
HB 12
HY 5
PI 1
CLASH 5
⚠ Exposure 53%
Interaction summary
HB 12
HY 5
PI 1
CLASH 5
⚠ Exposure 53%
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (8/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 15
Buried (contacted) 7
Exposed 8
LogP 3.3
H-bonds 12
Exposed fragments:
phenyl (2/5 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.378 | Score | -21.303 |
|---|---|---|---|
| Inter norm | -1.174 | Intra norm | 0.159 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
MET78
SER46
THR74
TYR49
| ||
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 16 | Native recall | 0.94 |
| Jaccard | 0.84 | RMSD | - |
| HB strict | 10 | Strict recall | 0.77 |
| HB same residue+role | 8 | HB role recall | 0.73 |
| HB same residue | 8 | HB residue recall | 0.73 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 402 | 1.2167690104404725 | -1.34895 | -25.6842 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 485 | 1.4860261846578509 | -1.05884 | -19.9656 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 425 | 2.519301932614363 | -1.38873 | -28.5459 | 10 | 15 | 5 | 0.29 | 0.27 | - | no | Open |
| 418 | 3.3781155952566757 | -1.17369 | -21.3034 | 12 | 18 | 16 | 0.94 | 0.73 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.303kcal/mol
Ligand efficiency (LE)
-1.0144kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.653
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
294.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.30
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
14.59kcal/mol
Minimised FF energy
6.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
539.3Ų
Total solvent-accessible surface area of free ligand
BSA total
424.9Ų
Buried surface area upon binding
BSA apolar
283.4Ų
Hydrophobic contacts buried
BSA polar
141.4Ų
Polar contacts buried
Fraction buried
78.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2122.1Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
656.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)