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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
14.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.90, Jaccard 0.73, H-bond role recall 0.36
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
61% of hydrophobic surface is solvent-exposed (14/23 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
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.931 kcal/mol/HA)
✓ Good fit quality (FQ -8.98)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Moderate strain (14.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-27.931
kcal/mol
LE
-0.931
kcal/mol/HA
Fit Quality
-8.98
FQ (Leeson)
HAC
30
heavy atoms
MW
413
Da
LogP
5.30
cLogP
Interaction summary
HB 6
HY 9
PI 1
CLASH 5
⚠ Exposure 60%
Interaction summary
HB 6
HY 9
PI 1
CLASH 5
⚠ Exposure 60%
Solvent-exposed hydrophobic surface — desolvation penalty likely
61% of hydrophobic surface is solvent-exposed (14/23 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 23
Buried (contacted) 9
Exposed 14
LogP 5.3
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.738 | Score | -27.931 |
|---|---|---|---|
| Inter norm | -1.037 | Intra norm | 0.106 |
| Top1000 | no | Excluded | no |
| Contacts | 24 | H-bonds | 6 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ALA158
ALA24
ALA40
ALA70
ASN126
ASN41
ASP129
ASP68
GLN42
GLU73
GLY23
GLY25
GLY71
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
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 | 19 | Native recall | 0.90 |
| Jaccard | 0.73 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 575 | 1.0399056885554303 | -0.751969 | -21.6104 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 575 | 1.2383004177190995 | -0.879713 | -24.9612 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 593 | 1.840988622981869 | -0.872435 | -23.9498 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 601 | 2.3276582312652585 | -0.752765 | -24.4998 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 2.6007481059821833 | -0.753229 | -21.5097 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 599 | 2.7382383736726044 | -1.03726 | -27.9313 | 6 | 24 | 19 | 0.90 | 0.36 | - | no | Current |
| 594 | 3.260885981020757 | -0.879028 | -23.4199 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 3.268899464166515 | -1.08062 | -31.5572 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 605 | 4.277421972823018 | -0.921936 | -26.7502 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 587 | 4.87930352531888 | -1.00805 | -27.8762 | 7 | 17 | 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
-27.931kcal/mol
Ligand efficiency (LE)
-0.9310kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.981
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
413.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.30
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.69kcal/mol
Minimised FF energy
43.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
693.8Ų
Total solvent-accessible surface area of free ligand
BSA total
627.8Ų
Buried surface area upon binding
BSA apolar
458.5Ų
Hydrophobic contacts buried
BSA polar
169.3Ų
Polar contacts buried
Fraction buried
90.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.0%
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
497.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)