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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
30.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.90, Jaccard 0.76, H-bond role recall 0.45
Reason: 1 severe internal clashes
1 severe internal clashes
5 protein-contact clashes
5 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.027 kcal/mol/HA)
✓ Good fit quality (FQ -10.01)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Very high strain energy (30.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-31.848
kcal/mol
LE
-1.027
kcal/mol/HA
Fit Quality
-10.01
FQ (Leeson)
HAC
31
heavy atoms
MW
478
Da
LogP
4.72
cLogP
Final rank
4.1042
rank score
Inter norm
-1.066
normalised
Contacts
23
H-bonds 11
Interaction summary
HBD 1
HBA 6
HY 3
PI 1
CLASH 5
Severe 1
Interaction summary
HBD 1
HBA 6
HY 3
PI 1
CLASH 5
Severe 1
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 | 19 | Native recall | 0.90 |
| Jaccard | 0.76 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 460 | 1.8777448127256184 | -0.865635 | -19.3746 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 477 | 1.9436046199643353 | -0.914653 | -22.7513 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 462 | 2.013375696079133 | -0.764934 | -21.3119 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 452 | 2.316087839707507 | -1.17716 | -58.3646 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 496 | 2.3705378259640018 | -0.863559 | -25.661 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 2.489012354934417 | -1.16168 | -31.9315 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 2.6908538270493585 | -0.830365 | -21.085 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 465 | 2.715181301617068 | -0.904736 | -19.1684 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 2.8199088495293476 | -0.821603 | -22.806 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 478 | 4.104156564970094 | -1.06645 | -31.8476 | 11 | 23 | 19 | 0.90 | 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
-31.848kcal/mol
Ligand efficiency (LE)
-1.0273kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.009
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
478.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.72
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-11.56kcal/mol
Minimised FF energy
-42.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
705.2Ų
Total solvent-accessible surface area of free ligand
BSA total
598.0Ų
Buried surface area upon binding
BSA apolar
444.5Ų
Hydrophobic contacts buried
BSA polar
153.6Ų
Polar contacts buried
Fraction buried
84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1373.1Ų
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
532.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)