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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
13.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.73, H-bond role recall 0.45
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.355 kcal/mol/HA)
✓ Good fit quality (FQ -12.48)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (13.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-35.225
kcal/mol
LE
-1.355
kcal/mol/HA
Fit Quality
-12.48
FQ (Leeson)
HAC
26
heavy atoms
MW
372
Da
LogP
2.94
cLogP
Interaction summary
HB 14
HY 15
PI 1
CLASH 3
⚠ Exposure 42%
Interaction summary
HB 14
HY 15
PI 1
CLASH 3
⚠ Exposure 42%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 11
Exposed 8
LogP 2.94
H-bonds 14
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.280 | Score | -35.225 |
|---|---|---|---|
| Inter norm | -1.469 | Intra norm | 0.114 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 14 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes | ||
| Residues |
ALA24
ALA40
ASN41
GLN42
GLU21
GLU73
GLY23
GLY25
LEU39
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
THR44
| ||
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 | 0.73 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 506 | 0.4754442014664873 | -0.866465 | -17.7436 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 499 | 0.6625064591564637 | -1.01915 | -20.2949 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 474 | 3.0237680125739086 | -0.972343 | -19.2689 | 4 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 461 | 3.8456029025782232 | -1.08628 | -23.2623 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 484 | 4.070340177265735 | -0.975432 | -21.9677 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 4.280190594778117 | -1.46863 | -35.2248 | 14 | 17 | 16 | 0.76 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-35.225kcal/mol
Ligand efficiency (LE)
-1.3548kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.482
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
372.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.94
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-72.66kcal/mol
Minimised FF energy
-85.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.0Ų
Total solvent-accessible surface area of free ligand
BSA total
525.0Ų
Buried surface area upon binding
BSA apolar
377.2Ų
Hydrophobic contacts buried
BSA polar
147.9Ų
Polar contacts buried
Fraction buried
83.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1318.0Ų
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
525.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)