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 mixed
SASA done
Strain ΔE
9.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.39, H-bond role recall 0.36
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
57% of hydrophobic surface appears solvent-exposed (8/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.642 kcal/mol/HA)
✓ Good fit quality (FQ -13.46)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (9.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-31.200
kcal/mol
LE
-1.642
kcal/mol/HA
Fit Quality
-13.46
FQ (Leeson)
HAC
19
heavy atoms
MW
256
Da
LogP
1.86
cLogP
Final rank
2.1250
rank score
Inter norm
-1.648
normalised
Contacts
18
H-bonds 13
Interaction summary
HBD 1
HBA 6
HY 2
PI 0
CLASH 5
Interaction summary
HBD 1
HBA 6
HY 2
PI 0
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.200kcal/mol
Ligand efficiency (LE)
-1.6421kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.460
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
256.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.86
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.96kcal/mol
Minimised FF energy
78.43kcal/mol
SASA & burial
✓ computed
SASA (unbound)
470.1Ų
Total solvent-accessible surface area of free ligand
BSA total
434.2Ų
Buried surface area upon binding
BSA apolar
327.6Ų
Hydrophobic contacts buried
BSA polar
106.5Ų
Polar contacts buried
Fraction buried
92.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1231.9Ų
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
500.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)