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
14.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.82, Jaccard 0.78, H-bond role recall 0.45
Reason: no major geometry red flags detected
2 protein-contact clashes
71% of hydrophobic surface is solvent-exposed (15/21 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.904 kcal/mol/HA)
✓ Good fit quality (FQ -8.44)
✓ Strong H-bond network (10 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Moderate strain (14.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.413
kcal/mol
LE
-0.904
kcal/mol/HA
Fit Quality
-8.44
FQ (Leeson)
HAC
27
heavy atoms
MW
390
Da
LogP
5.24
cLogP
Interaction summary
HB 10
HY 5
PI 1
CLASH 2
⚠ Exposure 71%
Interaction summary
HB 10
HY 5
PI 1
CLASH 2
⚠ Exposure 71%
Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (15/21 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 21
Buried (contacted) 6
Exposed 15
LogP 5.24
H-bonds 10
Exposed fragments:
phenyl (3/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 2.526 | Score | -24.413 |
|---|---|---|---|
| Inter norm | -0.923 | Intra norm | 0.019 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
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 | 14 | Native recall | 0.82 |
| Jaccard | 0.78 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 404 | 0.36981656016428793 | -0.921897 | -25.4787 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 469 | 0.7633901023181492 | -0.95056 | -25.8991 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 433 | 0.885640899780341 | -0.771777 | -17.9441 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 367 | 2.353859191578825 | -1.16083 | -30.0381 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 377 | 2.525823341113361 | -0.923206 | -24.4127 | 10 | 15 | 14 | 0.82 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.413kcal/mol
Ligand efficiency (LE)
-0.9042kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.436
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
389.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.24
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.80kcal/mol
Minimised FF energy
80.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
657.1Ų
Total solvent-accessible surface area of free ligand
BSA total
421.8Ų
Buried surface area upon binding
BSA apolar
264.0Ų
Hydrophobic contacts buried
BSA polar
157.8Ų
Polar contacts buried
Fraction buried
64.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2215.5Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
701.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)