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 mixed
SASA done
Strain ΔE
37.0 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.52, Jaccard 0.35, H-bond role recall 0.36
Reason: 8 internal clashes
8 protein-contact clashes
8 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.124 kcal/mol/HA)
✓ Good fit quality (FQ -10.35)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (37.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-29.219
kcal/mol
LE
-1.124
kcal/mol/HA
Fit Quality
-10.35
FQ (Leeson)
HAC
26
heavy atoms
MW
398
Da
LogP
2.65
cLogP
Interaction summary
HB 16
HY 8
PI 0
CLASH 8
⚠ Exposure 37%
Interaction summary
HB 16
HY 8
PI 0
CLASH 8
⚠ Exposure 37%
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
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 10
Exposed 6
LogP 2.65
H-bonds 16
Exposed fragments:
phenyl (4/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.415 | Score | -29.219 |
|---|---|---|---|
| Inter norm | -1.159 | Intra norm | 0.035 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 16 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes; high strain Δ 37.0 | ||
| Residues |
ALA24
ALA48
ALA70
ASP68
GLN42
GLU21
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LEU31
LEU39
LYS26
SER22
SER27
SER28
THR44
THR45
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 338 | 2.1801465777957825 | -0.758294 | -18.4464 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 305 | 2.596552910981433 | -0.967078 | -23.6974 | 6 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 351 | 2.6551293991681417 | -1.12903 | -26.9003 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 358 | 3.5547396501747 | -1.09509 | -24.6491 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 375 | 3.929077751592255 | -1.028 | -24.1661 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 294 | 4.415045767776549 | -1.15916 | -29.2189 | 16 | 21 | 11 | 0.52 | 0.36 | - | no | Current |
| 253 | 5.15382495728802 | -0.9244 | -23.1267 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.219kcal/mol
Ligand efficiency (LE)
-1.1238kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.354
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
397.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.65
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-56.38kcal/mol
Minimised FF energy
-93.42kcal/mol
SASA & burial
✓ computed
SASA (unbound)
651.7Ų
Total solvent-accessible surface area of free ligand
BSA total
588.8Ų
Buried surface area upon binding
BSA apolar
411.8Ų
Hydrophobic contacts buried
BSA polar
177.0Ų
Polar contacts buried
Fraction buried
90.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1336.2Ų
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
495.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)