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
15.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.343 kcal/mol/HA)
✓ Good fit quality (FQ -11.00)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (15.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.508
kcal/mol
LE
-1.343
kcal/mol/HA
Fit Quality
-11.00
FQ (Leeson)
HAC
19
heavy atoms
MW
279
Da
LogP
2.90
cLogP
Interaction summary
HB 10
HY 2
PI 1
CLASH 5
⚠ Exposure 53%
Interaction summary
HB 10
HY 2
PI 1
CLASH 5
⚠ Exposure 53%
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
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13
Buried (contacted) 6
Exposed 7
LogP 2.9
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.448 | Score | -25.508 |
|---|---|---|---|
| Inter norm | -1.460 | Intra norm | 0.117 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
TYR49
| ||
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 380 | 1.2157029303091844 | -1.31937 | -22.3757 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 365 | 2.03476027107978 | -1.69221 | -27.2831 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 492 | 2.149058578081181 | -1.23753 | -21.0928 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 344 | 2.4482415740067793 | -1.45975 | -25.5076 | 10 | 13 | 12 | 0.71 | 0.45 | - | no | Current |
| 368 | 2.7696457872585443 | -1.25917 | -21.824 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 377 | 3.074515803373726 | -1.38191 | -21.767 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 414 | 3.32166662867758 | -1.46812 | -21.6428 | 9 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 3.6859088691304858 | -1.28583 | -23.0255 | 8 | 14 | 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
-25.508kcal/mol
Ligand efficiency (LE)
-1.3425kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.004
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
278.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.90
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
68.33kcal/mol
Minimised FF energy
53.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
490.1Ų
Total solvent-accessible surface area of free ligand
BSA total
376.4Ų
Buried surface area upon binding
BSA apolar
281.4Ų
Hydrophobic contacts buried
BSA polar
94.9Ų
Polar contacts buried
Fraction buried
76.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2100.2Ų
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
711.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)