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
38.2 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.57, Jaccard 0.44, H-bond role recall 0.55
Reason: 7 internal clashes
7 protein-contact clashes
7 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (12/12 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.221 kcal/mol/HA)
✓ Good fit quality (FQ -10.78)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (79% SASA buried)
✗ Very high strain energy (38.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-28.085
kcal/mol
LE
-1.221
kcal/mol/HA
Fit Quality
-10.78
FQ (Leeson)
HAC
23
heavy atoms
MW
356
Da
LogP
0.33
cLogP
Final rank
4.8386
rank score
Inter norm
-1.312
normalised
Contacts
18
H-bonds 9
Interaction summary
HBD 1
HBA 6
HY 0
PI 0
CLASH 7
Interaction summary
HBD 1
HBA 6
HY 0
PI 0
CLASH 7
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 12 | Native recall | 0.57 |
| Jaccard | 0.44 | RMSD | - |
| HB strict | 8 | Strict recall | 0.53 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 6 | HB residue recall | 0.55 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 338 | 1.06286744963852 | -1.11607 | -26.3166 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 302 | 2.8980343327251057 | -1.24641 | -29.3864 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 304 | 3.616480702768086 | -1.26916 | -29.1696 | 16 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 331 | 4.838579541003643 | -1.31153 | -28.0852 | 9 | 18 | 12 | 0.57 | 0.55 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.085kcal/mol
Ligand efficiency (LE)
-1.2211kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.777
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.33
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-48.82kcal/mol
Minimised FF energy
-87.01kcal/mol
SASA & burial
✓ computed
SASA (unbound)
566.2Ų
Total solvent-accessible surface area of free ligand
BSA total
449.7Ų
Buried surface area upon binding
BSA apolar
262.7Ų
Hydrophobic contacts buried
BSA polar
187.0Ų
Polar contacts buried
Fraction buried
79.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
58.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1198.7Ų
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
510.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)