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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
43.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.55, H-bond role recall 0.18
Reason: strain 43.0 kcal/mol
strain ΔE 43.0 kcal/mol
4 protein-contact clashes
4 intramolecular 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.998 kcal/mol/HA)
✓ Good fit quality (FQ -9.72)
✓ Good H-bonds (5 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Extreme strain energy (43.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-30.928
kcal/mol
LE
-0.998
kcal/mol/HA
Fit Quality
-9.72
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
3.61
cLogP
Final rank
5.2851
rank score
Inter norm
-1.037
normalised
Contacts
24
H-bonds 7
Interaction summary
HBD 2
HBA 3
HY 4
PI 1
CLASH 4
Interaction summary
HBD 2
HBA 3
HY 4
PI 1
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.55 | RMSD | - |
| HB strict | 2 | Strict recall | 0.13 |
| HB same residue+role | 2 | HB role recall | 0.18 |
| 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 495 | 2.339943304433577 | -0.71396 | -22.534 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 461 | 2.627364265130163 | -0.762157 | -19.9349 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 453 | 3.3833864821800446 | -0.901799 | -24.1742 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 453 | 3.4830428225843786 | -0.911142 | -31.2285 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 469 | 5.28505895985913 | -1.03656 | -30.9282 | 7 | 24 | 16 | 0.76 | 0.18 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.928kcal/mol
Ligand efficiency (LE)
-0.9977kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.720
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
461.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.61
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
43.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
24.61kcal/mol
Minimised FF energy
-18.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
697.2Ų
Total solvent-accessible surface area of free ligand
BSA total
637.8Ų
Buried surface area upon binding
BSA apolar
503.9Ų
Hydrophobic contacts buried
BSA polar
133.9Ų
Polar contacts buried
Fraction buried
91.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1408.5Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
513.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)