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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
77.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.48, Jaccard 0.33, H-bond role recall 0.27
Reason: strain 77.2 kcal/mol
strain ΔE 77.2 kcal/mol
3 protein-contact clashes
3 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.318 kcal/mol/HA)
✓ Good fit quality (FQ -11.24)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Extreme strain energy (77.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-27.674
kcal/mol
LE
-1.318
kcal/mol/HA
Fit Quality
-11.24
FQ (Leeson)
HAC
21
heavy atoms
MW
302
Da
LogP
-1.34
cLogP
Interaction summary
HB 16
HY 0
PI 0
CLASH 3
⚠ Exposure 100%
Interaction summary
HB 16
HY 0
PI 0
CLASH 3
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
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.
Non-polar atoms 12
Buried (contacted) 0
Exposed 12
LogP -1.34
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.821 | Score | -27.674 |
|---|---|---|---|
| Inter norm | -1.453 | Intra norm | 0.135 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 16 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 77.1 | ||
| Residues |
ALA24
ALA70
ASP68
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LEU31
LYS26
SER22
SER27
SER28
THR44
THR69
| ||
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 | ||
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 | 10 | Native recall | 0.48 |
| Jaccard | 0.33 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
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
No hy · hydrophobic contacts detected for this pose.
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 630 | 1.4925265336114306 | -1.24603 | -31.9737 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 649 | 3.8213105660036932 | -1.45275 | -27.6741 | 16 | 19 | 10 | 0.48 | 0.27 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.674kcal/mol
Ligand efficiency (LE)
-1.3178kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.240
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
302.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.34
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
77.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
197.67kcal/mol
Minimised FF energy
120.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
460.8Ų
Total solvent-accessible surface area of free ligand
BSA total
436.4Ų
Buried surface area upon binding
BSA apolar
292.9Ų
Hydrophobic contacts buried
BSA polar
143.6Ų
Polar contacts buried
Fraction buried
94.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1189.1Ų
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
488.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)