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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
24.9 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.67, Jaccard 0.50, H-bond role recall 0.45
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.408 kcal/mol/HA)
✓ Good fit quality (FQ -12.42)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (24.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-32.375
kcal/mol
LE
-1.408
kcal/mol/HA
Fit Quality
-12.42
FQ (Leeson)
HAC
23
heavy atoms
MW
333
Da
LogP
2.67
cLogP
Interaction summary
HB 11
HY 2
PI 0
CLASH 6
Interaction summary
HB 11
HY 2
PI 0
CLASH 6
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 4.755 | Score | -32.375 |
|---|---|---|---|
| Inter norm | -1.369 | Intra norm | -0.038 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 11 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes; moderate strain Δ 24.9 | ||
| Residues |
ALA24
ALA40
ALA70
ASN41
ASP68
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
LEU39
LYS127
LYS26
SER22
SER27
SER28
THR44
THR69
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 14 | Native recall | 0.67 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 508 | 4.754727446128632 | -1.36927 | -32.3748 | 11 | 21 | 14 | 0.67 | 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
-32.375kcal/mol
Ligand efficiency (LE)
-1.4076kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.423
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
333.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.67
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-18.44kcal/mol
Minimised FF energy
-43.33kcal/mol
SASA & burial
✓ computed
SASA (unbound)
536.4Ų
Total solvent-accessible surface area of free ligand
BSA total
481.2Ų
Buried surface area upon binding
BSA apolar
391.6Ų
Hydrophobic contacts buried
BSA polar
89.6Ų
Polar contacts buried
Fraction buried
89.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1314.7Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
495.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)