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 strong
SASA done
Strain ΔE
82.5 kcal/mol
Protein clashes
15
Internal clashes
15
Native overlap
contact recall 0.81, Jaccard 0.61, H-bond role recall 0.45
Reason: 15 protein-contact clashes, 15 internal clashes, strain 82.5 kcal/mol
strain ΔE 82.5 kcal/mol
15 protein-contact clashes
15 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.020 kcal/mol/HA)
✓ Good fit quality (FQ -9.84)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Extreme strain energy (82.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-30.588
kcal/mol
LE
-1.020
kcal/mol/HA
Fit Quality
-9.84
FQ (Leeson)
HAC
30
heavy atoms
MW
449
Da
LogP
2.29
cLogP
Final rank
6.4402
rank score
Inter norm
-1.085
normalised
Contacts
24
H-bonds 10
Interaction summary
HBD 1
HBA 6
HY 4
PI 1
CLASH 15
Interaction summary
HBD 1
HBA 6
HY 4
PI 1
CLASH 15
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| 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 | 17 | Native recall | 0.81 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 314 | 1.390735705254885 | -1.10855 | -27.381 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 1.8804357488178156 | -0.799671 | -26.0217 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 410 | 2.8379713428906985 | -0.949485 | -30.703 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 3.0760476938939365 | -0.878694 | -30.7024 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 328 | 6.440190195508428 | -1.08489 | -30.5882 | 10 | 24 | 17 | 0.81 | 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
-30.588kcal/mol
Ligand efficiency (LE)
-1.0196kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.835
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
448.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.29
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
82.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-12.13kcal/mol
Minimised FF energy
-94.65kcal/mol
SASA & burial
✓ computed
SASA (unbound)
677.7Ų
Total solvent-accessible surface area of free ligand
BSA total
597.8Ų
Buried surface area upon binding
BSA apolar
417.7Ų
Hydrophobic contacts buried
BSA polar
180.1Ų
Polar contacts buried
Fraction buried
88.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1343.4Ų
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
503.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)